Single Cell Expression Atlas release 21 – September 2024

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
• This release contains 383 single cell RNA-Seq studies, consisting of 17,846,119 cells, of which 10,053,044 passed our QC from 21 different species.

Software features

• Gut anatomogram - a new human anatomogram for the large and small intestines has been added in this release and accompanies eligible experiments, e.g. E-GEOD-125970
• Inferred cell type marker gene heatmap - for experiments where inferred cell type data is available you can now view marker genes based on the inferred cell type clusters, e.g. E-GEOD-227038
• Multiple Resources links are now made available to users where applicable, e.g. E-MTAB-10287

New experiments

Highlights

• Externally analysed data - in this release we have included an entirely new class of data to Single Cell Expression Atlas - externally analysed data, marked with an ‘E’ icon. These are currently limited to a careful selection of eligible high-impact human datasets including the GTEx: snRNAseq atlas As these experiments are not re-analysed with our own analysis pipelines, not all the standard chart or data options may be available
• Important resource for studying aging in the model organism Drosophila melanogaster Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution
• The human gastrointestinal tract through space and time - Adult GEX
• Single-cell RNA-seq of germinating Arabidopsis thaliana seeds

Externally analysed datasets

• Human Lung Cell Atlas: An integrated cell atlas of the human lung in health and disease
• GTEx: snRNAseq atlas
• Tabula Sapiens - Smart-seq2 dataset
• Mapping the developing human immune system across organs

Datasets reanalysed with our standard pipelines

• Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions
• Organogenetic transcriptomes of the Drosophila embryo at single cell resolution
• Single cell RNA-sequencing of normal and fibrotic lungs in human
• A single-cell transcriptome of the developing visceral muscle of Drosophila melanogaster embryo.
• microRNA-252 and FoxO repress inflammaging by a dual inhibitory mechanism on Dawdle mediated TGF-β pathway in Drosophila muscle
• A combinatorial code of transcription factors specifies subtypes of visual motion-sensing neurons in Drosophila
• Trajectory Mapping of the Early Drosophila Germline Reveals Controls of Zygotic Activation and Sex Differentiation
• The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis
• Transcriptional programs of circuit assembly in the Drosophila visual system
• Reactive oligodendrocyte progenitor cells (re-)myelinate the regenerating zebrafish spinal cord [Single cell]
• A comprehensive series of temporal transcription factors in the fly visual system
• A lymphocyte-microglia-astrocyte axis in chronic active multiple sclerosis
• Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution
• Transcriptomic analysis of REPTOR or FoxO increased activity in muscle tissue using single nuclear RNA-seq analysis of Drosophila thoraces
• Single-cell sequencing of stage 4 chicken embryos
• GM-CSF-producing T helper cells: a distinct subset of T helper cells.
• Time-resolved single-cell analysis of Brca1 associated mammary tumorigenesis reveals aberrant differentiation of luminal progenitors
• Unraveling Transcriptomic Heterogeneity in the Human Dermal Blood Vascular Endothelium at Single-Cell Resolution
• Single-cell RNA-seq of Endometrial Superficial biopsies and full depth uterine tissue from organ donors
• Single cell RNA-seq of Pgc+ cells in homeostasis and upon injury
• Single-cell transcriptional profiling of primary human dental follicle and derived organoids
• Fly Cell Atlas: single-cell transcriptomes of the entire adult Drosophila - Smartseq2 dataset
• scRNA-seq of human fetal lung explants with R-SPONDIN inhibition and human fetal lung primary tissue
• Single-cell RNA-seq of germinating Arabidopsis thaliana seeds
• Single cell RNAseq of wild-type and Iqgap2-/- (KO) mouse brain endothelial cells
• Single nucleus RNA sequencing in mouse brown adipose tissue at room temperature, cold condition and thermoneutrality
• Single-cell RNA-seq of Drosophila embryos to investigate gene expression during dorsal-ventral patterning
• The human gastrointestinal tract through space and time - Adult GEX

Single Cell Expression Atlas release 20 – March 2023

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
• This release contains 355 single cell RNA-Seq studies, consisting of 17,469,458 cells, of which 10,505,726 passed our QC from 21 different species.

New experiments

New species! Xenopus tropicalis

• single cell RNAseq on isolated spinal cord cells before and 3 day post tail amputation in Xenopus tropicalis tadpoles at stage NF50

Homo sapiens

• Single cell RNAseq of ankylosing spondylitis lymphocytes from peripheral blood and synovial fluid
• Cross-tissue immune cell analysis reveals tissue-specific features in humans
• Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes
• The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy
• Single cell transcriptome atlases of the developing mouse and human spinal cord - human data
• Single cell analysis of emergent haematopoiesis in the human fetal bone marrow (10X)
• Single-cell RNA-seq of Endometrial organoids treated with NOTCH or WNT inhibitors in a time course of Estrogen and Progesterone stimulation
• Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk
• 10x scRNA-seq analysis of a human milk cell sample compared to a non-lactating breast tissue sample
• Single-Cell RNA Sequencing of Retinal Organoids Derived by CSC14 hESCs
• The atlas of the human hypertrophied heart reveals impaired cell communication
• Single cell RNA-seq of in vitro cultured human embryos
• Single-cell RNA-seq of human peripheral blood mononuclear cells (PBMCs) throughout the febrile, critical, and convalescence phases of dengue virus infection
• scRNA-seq analysis of human mammary epithelial cells derived from non-lactating breast tissue or from milk
• Single-cell transcriptional profiling of young-adult and aging (middle-aged) mouse anterior pituitary in steady-state conditions and after transgenically inflicted local damage
• Single Cell Transcriptional and Chromatin Accessibility Profiling on the human adult kidneys
• Comparative analysis of kidney organoid and adult human kidney single cell and single nucleus transcriptomes - human kidney subset

Mus musculus

• Single-cell sequencing of epicardial cells and fibroblasts within the infarcted heart
• scRNA-Seq analysis of differentiation to primitive streak fate of mouse embryonic stem cells
• Melanoma-derived extracellular vesicles mediate lymphatic remodeling and impair tumor immunity in draining lymph nodes
• Single cell RNA sequencing of myeloid cells from the aortas of ApoE-/- mice fed a high fat diet for 12-16 weeks
• Single cell RNA sequencing of myeloid cells from the aortas of ApoE-/- and ApoE-/- Clec4a2-/- mice fed a high fat diet for 12 weeks
• Single nucleus RNAseq of mouse inguinal white adipose tissue with Rspo2 or GFP AAV injection
• Single cell RNA sequencing of intestinal NKp46+ innate lymphoid cells (ILCs) from Hif1a(fl/fl) and Ncr1(Cre)Hif1a(fl/fl) mice
• RNA-seq of coding RNA from single cells derived from mouse embryos
• RNA-seq to assess the impact of circulation on hematopoietic stem cell differentiation
• Changes in Pdgfra-positive mesenchymal progenitors during muscle regeneration under normal and obese condition
• Single cell RNA-seq of pancreatic mouse tumors upon treatment
• Tracing the emergence of primordial germ cells from bilaminar disc rabbit embryos and pluripotent stem cells (embryo single cell RNA-sequencing)

Drosophila melanogaster

• Single-cell RNA sequencing of Drosophila melanogaster optic lobe cells
• Drosophila melanogaster female late third instar larval gonads single-cell RNA-Seq (scRNA-Seq) profiling
• Modular transcriptional programs separately define axon and dendrite connectivity
• Single-cell RNA sequencing of escort cells (ECs) in Drosophila ovaries
• A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord
• Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
• The Drosophila Brain on Cocaine at Single Cell Resolution
• Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells
• Adult Phenotypes and Gene Expression in the Brain at Single Cell Resolution After Developmental Alcohol Exposure in Drosophila
• Drosophila voltage-gated sodium channels are only expressed in active neurons and are localized to distal axonal initial segment-like domains
• Neuronal diversity and convergence in a visual system developmental atlas part 2

Oryctolagus cuniculus

• Single-cell RNA-seq of of bone marrow derived mononuclear phagocytes derived from rat

Danio rerio

• Single-cell RNA sequencing of zebrafish thyroid cells
• Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma [scRNA-Seq]
• Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae
• Single-cell profiling of photoreceptor cells in adult zebrafish
• Analysis of single CD41 cell transcriptomes from Zebrafish
• Single-cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish
• Modeling Notch-induced tumor cell survival in the Drosophila ovary identifies cellular and transcriptional response to nuclear NICD accumulation

Rattus norvegicus

• Single-cell RNA-seq of rat microglia in monoculture and in coculture with neurons and astrocytes

Single Cell Expression Atlas release 19 – March 2022

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
• This release contains 304 single cell RNA-Seq studies, consisting of 13,826,582 cells, of which 8,524,149 passed our QC from 20 different species.

New features

• All datasets now include an standardised AnnData object downloadable from the FTP.
• Two new species: Oryctolagus cuniculus and Ovis aries.
• New collection for experiments from the discovAIR project, it currently contains four experiments with more coming soon:
  • Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
  • Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium (in vivo)
  • Ischaemic sensitivity of human tissue by single cell RNA seq
  • Lung Cell Atlas: Single cell RNA sequencing analysis of fresh resected human lung tissue - Drop-seq dataset

New experiments

Fly Cell Atlas datasets:

• Fly Cell Atlas: single-cell transcriptomes of the entire adult Drosophila - 10x dataset
• Fly Cell Atlas: single-cell transcriptomes of the entire adult Drosophila - Smartseq2 dataset

Other datasets:

• Single-cell RNA-seq of of bone marrow derived mononuclear phagocytes derived from mouse
• Single-cell RNA-seq of of bone marrow derived mononuclear phagocytes derived from rabbit
• Single cell analysis of emergent haematopoiesis in the human fetal bone marrow (10X)
• Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium (in vivo)
• Single cell RNA-seq of B cells from sheep red blood cells-primed WT and Stch cKO mice
• Single-cell immune repertoire sequencing of bone marrow plasma cells following infection and immunizations
• Gene expression atlas of Drosophila wing disc by single cell expression correlation analysis - 10x dataset
• Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes
• A single-cell transcriptome atlas of the ageing Drosophila brain - Drop-seq dataset
• A single-cell transcriptome atlas of the ageing Drosophila brain - 10x dataset
• A single-cell transcriptome atlas of the ageing Drosophila brain - Smart-seq2 dataset
• Single-cell transcriptome sequencing from mouse mTECs
• Clonally expanded EOMES+ Tr1-like cells in primary and metastatic tumors associate with disease progression
• Single-cell RNA-seq of CD4+ Treg and Tmem cells from different tissues in mouse
• Single-cell RNA-seq of CD4+ Treg and Tmem cells from different tissues in human
• Single Cell Transcriptome of Human Fetal Liver
• The emergent landscape of the mouse gut endoderm at single-cell resolution
• Single-cell RNA-seq of Drosophila melanogaster male late third instar larval gonads
• Single cell transcriptome atlas of the Drosophila larval brain
• Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
• Single cell RNA sequencing of naive and primed human pluripotent stem cells treated with SB431542
• Haematopoietic stem and progenitor cells are present in healthy gingiva tissue
• RNA-seq of C57BL/6 mice splenocytes during Trypanosoma Evansi infection
• ScRNA-seq of dendritic cells from mouse lymph nodes
• Gremlin 1+ fibroblastic niche maintains dendritic cell homeostasis in lymphoid tissues
• scRNA-seq of stromal vascular cells from 48 week (aged) mouse subcutaneous adipose tissue compared to control 10 week (young) mouse SVF
• scRNA-seq of sheep abomasal epithelial tissue post-nematode infection
• Single-cell RNA-seq of fibroblasts influenced by exosomes derived from melanoma cell line G361
• Effects of Post-Myocardial Infarction Heart Failure on the Bone Vascular Niche (Human Data)
• Effects of Post-Myocardial Infarction Heart Failure on the Bone Vascular Niche (Mouse Data)
• The extracellular function of LGALS3BP in neural progenitors during brain development
• Single-cell RNA sequencing of human liver cells
• The host & gut microbiome orchestrate smoking cessation-induced weight gain
• scRNA-seq of E9.5 para-aortic splanchnopleura from NCX1-null embryos and wild type controls
• Single-Cell Transcriptomics Sheds Light on the Identity and Metabolism of Developing Arabidopsis Leaf Cells
• Single Cell Analysis of B cells in COVID-19 comprising active and recovered disease
• scRNAseq of Mus musculus ileum samples with RET melanoma against non-xenograft mice controls
• Gene expression pattern of single mES cells during cell cycle stages
• Single-cell RNA-seq of blastomeres from 2- to 32-cell stage mouse embryos
• Gene expression profiling of mouse liver cells
• Single-cell RNA-seq reveal lineage formation and X-chromosome dosage compensation in human preimplantation embryos
• Single-cell RNA sequencing of mouse embryos with Tal1 (Scl) knockout in gastrulation
• Single-cell RNA-sequencing resolves a CD4+ T cell fate bifurcation
• Single-cell RNA-seq of mouse CD4+ T-helper 2 cells from mediastinal lymph nodes
• Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE
• Single-cell RNA sequencing of mouse embryonic stem cells expressing 2-cell stage markers MERVL and Zscan4
• Retinoic acid mediated neural and mesoderm specification during vertebrate trunk development
• Single-cell RNA-seq of motor neuron progenitors differentiated from mouse embryonic stem cell line HM1 by treatment with retinoic acid (RA) and Sonic Hedgehog Signaling Agonist (SAG)
• Single-cell RNA-seq analysis of LPS- and palmitate-stimulated THP-1 macrophages
• Transcriptional disorganization of fibroblasts is a hallmark of the aging heart
• Single cell RNA sequencing analysis of mouse resident and infiltrating immune cells during acute kidney injury and fibrosis
• Single cell RNA-seq of human breast skin cells
• Single cell sequencing of renal endothelial cell heterogeneity and metabolic transcriptome adaptation to dehydration
• Single-cell RNA sequencing of hPSC-derived endothelial-to-haematopoietic transition
• Context-specific regulation of monocyte surface IL7R expression and soluble receptor secretion by a common autoimmune risk allele
• Regulation of transcriptional states in acute liver failure by microbiome
• Single cell RNA-seq of mouse E10.5 progenitor and E14.5 barrelette neurons
• Single RNA-Seq of synovial tissue macrophages from Rheumatoid Arthritis patients with active disease and in disease remission
• Ontogenic changes in hematopoietic hierarchy determine pediatric specificity and disease phenotype in fusion oncogene-driven myeloid leukemia - scRNAseq - 2
• Single cell RNA Seq of cortex cells from adult human ovaries
• Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes
• Human dendritic cell subsets in acute skin inflammation
• scRNAseq of Cyp11a1-expressing cells from mouse melanoma model derived tumors
• Single-cell RNA-seq of intestinal crypts of Red2Kras and Red2Pi3k mice
• Single cell RNA sequencing of chronic myelomonocytic leukemia stem cell
• Single-cell RNA-seq of the human fetal lateral ganglionic eminence at 7
• A spatially resolved single cell atlas of human gastrulation
• Single cell RNA sequencing of three IDHwt glioblastoma patient tumors
• Single cell transcriptional profile of third instar larval wing discs in Drosophila
• Single-cell RNA-seq on enriched cardiac fibroblasts from the healthy, sham or MI hearts of Hif-1a conditional knockout or heterozygous mice
• Single cell RNA-seq of human RPE1-MYCN-ER cells with treatment of EtOH (0h) or tamoxifen for 22h
• Single cell analysis of emergent haematopoiesis in the human fetal bone marrow (SS2)
• scRNA-seq of human fetal intestinal ileum tissue

Single Cell Expression Atlas release 18 – September 2021

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 229 single cell RNA-Seq studies, consisting of 8,478,751 cells, of which 5,978,348 passed our QC from 18 different species.

New experiments

• Single-cell RNA-seq of tumor-infiltrating lymphocytes in metastatic uveal melanoma
• A Cell Atlas of the Drosophila ovary
• Single-cell RNA sequencing of adult Drosophila ovary identifies transcriptional programs governing oogenesis
• A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants
• Transcriptomic and clonal characterization of T cells in the human central nervous system.
• Single cell RNA-seq of metabolite specific T-cells (MR1-restricted) from adult mouse thymus
• Liquid Biopsy-Based Single-Cell Transcriptome Profiling Characterizes Heterogeneity of Disseminated Tumor Cells from Lung Adenocarcinoma
• Single cell RNA-seq of 3 key time points in oesophageal post-natal development
• snRNA-seq of whole hearts from adult fzt:DU mice
• snRNA-seq of whole hearts from adult BL6 mice
• Single cell RNAseq of 12-week old AKIMBA versus WT mouse retina
• Single cell transcriptomics of iPSC derived neurons under genetic and toxic stressors

Single Cell Expression Atlas release 17 – August 2021

This is a software release only, so no new datasets have been added or updated.

New features

• UMAP plots: this release introduces the use of UMAP plotting for dimensionality reduction, adding this as an alternative to existing tSNE plots.
• Performance improvements, leading to faster loads of plots from database and index.

Single Cell Expression Atlas release 16 – May 2021

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 217 single cell RNA-Seq studies, consisting of 7,723,982 cells, of which 5,312,183 passed our QC from 18 different species.

New experiments

COVID-19 datasets

• A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients

Plant datasets

• Single-cell transcriptomic analysis of rice root tips – Oryza sativa Japonica Group
• Single-cell transcriptomic analysis of rice root tips – Oryza sativa Indica Group
• A single-cell analysis of the Arabidopsis vegetative shoot apex
• Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing
• Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
• Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery
• Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root
• Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex - snRNAseq
• Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex -scRNAseq
• Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions - scRNAseq of Arabidopsis thaliana root
• Single cell sequencing reveals phloem loading occurs via the abaxial bundle sheath cells in maize leaves
• A single cell view of the transcriptome during lateral root initiation of Arabidopsis thaliana
• Distinct identities of leaf phloem cells revealed by single cell transcriptomics

Other

• A cell atlas of human thymic development defines T cell repertoire formation
• A cell atlas of human thymic development defines T cell repertoire formation
• 10x single cell gene expression of T cells from the blood
• Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons
• Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics
• A single-cell survey of the human first-trimester placenta and decidua (Drop-seq)
• A single-cell survey of the human first-trimester placenta and decidua (10x)
• A human single cell atlas of the substantia nigra reveals novel cell specific pathways associated with the genetic risk of Parkinson’s disease and neuropsychiatric disorders
• Massively parallel single-cell RNA-seq analysis of pancreatic islets cells from both healthy and type II diabetic donors
• Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human
• Neuronal vulnerability and multilineage diversity in multiple sclerosis
• Single-cell transcriptome analysis reveals dynamic cell populations and differential gene expression patterns in control and aneurysmal human aortic tissue
• A single cell atlas of the human proximal epididymis reveals cell-type specific functions and distinct roles for CFTR
• Myocardial infarction time series single cell RNA-Seq
• Unravelling the heterogeneity of haemogenic endothelium in human pluripotent stem cell differentiation cultures
• Single-cell RNA sequencing of the human biliary tree
• Mouse brown adipocyte single nucleus RNAseq with Smartseq2
• Somatic Gain-of-Function mTOR mutation in Clonally Expanded T-lymphocytes Associated with Chronic Graft-Versus-Host Disease
• Integrative single-cell RNA-Seq and ATAC-Seq analysis of human foetal liver and bone marrow haematopoiesis (scRNA-Seq)

New features

This is a data release and includes no changes to the Single Cell Expression Atlas application.

Single Cell Expression Atlas release 15 – March 2021

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 184 single cell RNA-Seq studies, consisting of 5,890,292 cells, of which 4,104,531 passed our QC from 14 different species.

New experiments

• Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia (scRNA-seq: olfactory bulb)
• Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia (scRNA-seq: olfactory mucosa)
• Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni

New features

The main purpose of this data release is to improve the ontology based annotations that power the new organ anatomograms.

Single Cell Expression Atlas release 14 – February 2021

This is a software release only, so no new datasets have been added or updated

New features

• New interactive organ anatomograms for liver, lung, pancreas and placenta allow users to explore expression in cell types as they look into different organism parts and cell scaffolds within this organs. Approximately 9 experiments in Single Cell Expression Atlas, that have the required level of annotation, include anatomograms. Some examples below:
  • Lung Cell Atlas: Single cell RNA sequencing analysis of fresh resected human lung tissue
  • Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics
  • Single cell transcriptomics defines human islet cell signatures and reveals cell-type-specific expression changes in type 2 diabetes
• Organ anatomograms are accompanied by interactive cell type heatmaps, which react to selections in the anatomogram to display average cell type expression for marker genes.
• tSNE plot by default colours cells by inferred cell type, if available.
• tSNE plot and expression heatmaps can be exported as images, regardless of the size.
• Datasets have links to GEO/ENA

Single Cell Expression Atlas release 13 – December 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 181 single cell RNA-Seq studies, consisting of 5,775,820 cells, of which 4,037,874 passed our QC from 14 different species.

New experiments

• Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing
• Drop-seq single-cell sequencing of hemocytes from Drosophila larvae after wasp infestation
• scRNA-seq of Anopheles gambiae hemocytes after blood-feeding
• A single cell transcriptome atlas of myeloid blood cell lineages in Drosophila [scRNA-seq]
• Single cell RNA on hemocytes from wandering larvae of Drosophila melanogaster not infested and infested by Leptopilina boulardi
• Single cell RNA-Seq of the mouse heart in response to chronic stress

Single Cell Expression Atlas release 12 – October 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 175 single cell RNA-Seq studies, consisting of 5,457,628 cells, of which 3,804,907 passed our QC from 15 different species.

New experiments

Three new datasets relating to COVID-19:

• Gene expression profiling of SARS-CoV-1/2 infected human cell lines at single-cell level
• Immunophenotyping of COVID-19 and Influenza Underscores the Association of Type I IFN Response in Severe COVID-19
• RNA-seq of RBC depleted whole blood from COVID-19 patients and controls

Single Cell Expression Atlas release 11 – August 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 172 single cell RNA-Seq studies, consisting of 5,053,431 cells, of which 3,523,470 passed our QC from 14 different species.
• The aim of this release was to deliver updates in our analysis pipeline, performance improvements and inclusion of experiments collections for display.

New experiments

• Single-cell RNA-seq of nasal cavity mucosa cells of mice stimulated with interferon alpha
• A single-cell atlas of the peripheral immune response to severe COVID-19
• Single cell sequencing of developing heart valves identifies novel cell populations and uncovers interstitial cell heterogeneity
• Functional germ line stem cells do not exist in adult mammalian ovaries
• Single-cell RNA-seq of dermal fibroblasts (supplementary - human fibroblasts stimulation with dsRNA)
• Single-cell RNA-seq of dermal fibroblasts (5 human individuals - IFNB stimulation)
• Single-cell RNA-seq of human dermal fibroblasts (supplementary - different stimulation conditions of dsRNA)
• Single cell sequencing of colorectal tumors and adjacent non-malignant colon tissue

New features

• A new experiment collection for COVID-19 related research: Browse COVID-19 experiments
• In the experiment page, Supplementary Information tab, a section called Resources is available now for external resource links. These are resources potentially from ArrayExpress, GEO, ENA and EGA.
• A bug was fixed to allow users to download images for large tSNE plots, e.g.E-HCAD-14
• Marker Gene Heatmap: The marker gene symbols/IDs shown as row labels now act as hyperlinks, linking to the gene search result page within Single Cell Expression Atlas.
• In the Browse Experiments page, after checking the box to download the experiment and clicking the download link, a pop-up window now lets you select the file types (raw quantification, normalised counts or experimental design) to download.

Single Cell Expression Atlas release 10 – May 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 165 single cell RNA-Seq studies, consisting of 4,657,221 cells, of which 3,349,208 passed our QC from 14 different species.
• No new species, the aim of this release was to focus on COVID-19 related datasets and to use the new version 0.2.0 of our analysis pipeline:
  • Alevin updated to 1.2
  • Scanpy updated to 1.4.3, and tertiary workflow remodelled. As a result, many tSNE plots improved notably.
  • Marker p-values use BH correction rather than previous Bonferroni.
  • References properly reported and placed in bundles. Updated reference usage.

14 experiments relevant to the research of the current COVID-19 outbreak caused by the coronavirus SARS-Cov-2.

• Lung Cell Atlas: Single cell RNA sequencing analysis of fresh resected human lung tissue - Drop-seq dataset
• Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/macrophage populations
• Single-cell reconstruction of the early maternal-fetal interface in humans - Droplet
• Single-cell reconstruction of the early maternal-fetal interface in humans - SmartSeq2
• Spatiotemporal immune zonation of the human kidney
• Single cell RNA-seq of human pancreatic endocrine cells from juvenile, adult control and type 2 diabetic donors
• Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
• Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine
• Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]
• Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
• Human fetal liver, skin and kidney single cell transcriptome data
• scRNA-seq of human fetal lung primary tissues and cell cultures derived from fetal bud tip progenitors under dual SMAD treatment
• Ischaemic sensitivity of human tissue by single cell RNA seq
• The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty

New experiments

• Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
• Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine
• The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty
• Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
• Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]
• Single Cell RNA-sequencing of murine tail interfollicular epidermis basal cells at postnatal days 7
• Defining the Activated Fibroblast Population in Lung Fibrosis Using Single Cell Sequencing
• Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution
• A Cellular Atlas of Pitx2-Dependent Cardiac Development
• An integrated approach to profile lung tumor endothelial cell heterogeneity across species and models and to identify angiogenic candidates
• Single cell RNA-seq of a human ex vivo ovarian model with matched stromal cells
• Single cell RNA-seq from 10X for a living biobank of ovarian cancer ex vivo models reveals profound mitotic heterogeneity
• scRNA-seq analysis of lung CD64-expressing mononuclear cells, patrolling and classical monocytes from steady-state C57BL/6J mice
• scRNA-seq of human fetal lung primary tissues and cell cultures derived from fetal bud tip progenitors under dual SMAD treatment

Single Cell Expression Atlas release 9 – March 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
• This release contains 151 single cell RNA-Seq studies, consisting of 3,068,591 cells, of which 2,357,980 passed our QC from 14 different species.
• New species: Marmoset (Callithrix jacchus) and Plasmodium falciparum

New experiments

• Single cell transcriptomes of developing chicken hind limbs at stages HH25 - 10xv2 dataset
• Single cell transcriptomes of developing chicken hind limbs at stages HH25 - Dropseq dataset
• The Drosophila Embryo at Single-Cell Transcriptome Resolution - Drosophila melanogaster dataset
• Malaria Cell Atlas: Single cell transcriptomics of malaria parasites
• Immune landscape of viral- and carcinogen-derived head and neck cancer
• Single cell RNA expression of mouse embryonic basal forebrain
• Ischaemic sensitivity of human tissue by single cell RNA seq
• Spatio-temporal immune zonation of the human kidney
• Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
• Single cell profiling of human induced dendritic cells generated by direct reprogramming of embryonic fibroblasts
• Census of Immune Cells
• A single-cell reference map of transcriptional states for human blood and tissue T cell activation
• Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations
• Single-cell RNA sequencing of marmoset embryonic development
• Human fetal liver
• Single-cell transcriptional profiling of induced reprogramming trajectories
• Single-Cell Transcriptome Atlas of Murine Endothelial Cells
• Stromal evolution of cancer-associated fibroblasts in pancreatic ductal adenocarcinoma genetically engineered mouse models

New features

• Fully revamped experiments table: you can now apply multiple filters and sort by any column

Single Cell Expression Atlas release 8 – December 2019

Data statistics

• Ensembl 98 / Ensembl Genomes 45 / WormBase ParaSite 14 gene annotations.
• This release contains 132 single cell RNA-Seq studies, consisting of 1,306,531 cells, of which 1,020,169 passed our QC from 12 different species.
• New species: Chicken (Gallus gallus)

New experiments

• Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells and xenografts
• Single-cell RNA sequencing of lung adenocarcinoma patient-derived cells
• Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions [scRNA-seq]
• Single-cell sequencing of stage 4 chicken embryos
• Assessing the relevance of organoids to model inter-individual variation
• Profiling of CD34+ cells from human bone marrow to understand hematopoiesis
• Single-cell RNA-seq profiling of Drosophila melanogaster Rbf mutant third instar eye discs
• Single-cell RNA-seq on Drosophila melanogaster wild type third instar eye discs
• Single-cell RNA seq of mouse proximal small intestine at E16.5

Single Cell Expression Atlas release 7 – September 2019

Data statistics

• Ensembl 96 / Ensembl Genomes 43 / WormBase ParaSite 12 gene annotations.
• This release contains 123 single cell RNA-Seq studies, consisting of 1,214,110 cells, of which 946,724 passed our QC from 12 different species.

New experiments

• High-throughput single-cell transcriptome profiling of plant cell types - single cell dataset
• High-throughput single cell transcriptome profiling of plant tissue: single cell dataset
• Single-cell RNA-seq reveals differentiation hierarchy of normal human bone marrow and a distinct transcriptome signature of aneuploid cells
• Single Cell RNA sequencing of Adult Human Breast Epithelial Cells - individuals 1-3
• Multi-modal analysis of the aging mouse lung at cellular resolution
• Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation
• Single cell RNA-sequencing of human fetal kidneys
• Dynamics of gene expression in single root cells of Arabidopsis thaliana
• Single-cell RNA-sequencing analysis of Arabidopsis roots
• Neonatal and adult human testis defined at the single-cell level
• Single cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells
• Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [scRNA-seq]
• Lung Cell Atlas: Single cell RNA sequencing analysis of fresh resected human lung tissue - Drop-seq dataset
• Single cell analysis of human fetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors
• Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq
• Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
• A versatile approach for assessing human stem cell-derived retinal progeny using single cell transcriptomics
• Transcriptomic profile of human induced pluripotent stem cells at single cell resolution.
• scRNA-seq of Mus musculus subcutaneous Lin- cells derived from the subcutaneous adipose stromal vascular fraction
• Single cell RNA-seq of Stmn1+ isthmal cells and Pgc+ chief cells to compare and characterize distinct gastric corpus stem cells at molecular level
• scRNA-seq to investigate endoderm differentiation from induced human pluripotent stem cells
• Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp - single cell RNAseq dataset 1
• Single-cell RNA-seq of CD4+ Treg and Tmem cells from different tissues in mouse (Chromium 10x data)
• Single cell RNA-seq of adult human neural retina

Single Cell Expression Atlas release 6 – June 2019

Data statistics

• Ensembl 96 / Ensembl Genomes 43 / WormBase ParaSite 12 gene annotations.
• This release contains 99 single cell RNA-Seq studies, consisting of 882,958 cells, of which 513,317 passed our QC from 11 different species.

New experiments

• Malaria Cell Atlas: Single cell transcriptomics of malaria parasites
• Single-cell RNA-seq analysis of 20 organs and tissues from individual mice creates a Tabula muris
• Single cell transcriptomics defines human islet cell signatures and reveals cell-type-specific expression changes in type 2 diabetes
• Single cell RNA-seq before and after salt treatment in Saccharomyces cerevisiae
• Single cell RNA-seq of circulating breast cancer cells from 19 women with ER+/HER2- primary tumours
• Single cell RNA-seq of cancer stem cells from patients with chronic myeloid leukemia during the disease course
• Single cell RNA-seq of human pancreatic endocrine cells from Juvenile
• The Global Molecular Landscape of dormant Hematopoietic Stem Cells
• Single-cell RNA sequencing of spleen-derived LCK-expressing cells from adult zebrafish
• Lineage-dependent spatial and functional organisation of the mammalian enteric nervous system
• Deciphering the relationship between polycomb repression and stochastic gene expression from single-cell RNA-seq data
• Single-cell RNA-seq of murine medullary thymic epithelial cells (mTECs)
• scRNA-seq of mouse adipose stem and progenitor cells
• Single-cell RNA sequencing of OT-I CD8+ T cells after stimulation with different affinity ligands
• Single cell RNA-seq of isolated human foetal L/M-opsin cone photoreceptor populations labelled using the AAV2/9.pR2.1.GFP reporter
• Single cell RNA sequencing of stem cell-derived retinal ganglion cells
• Single cell RNA-Seq of the murine non-myocyte cardiac cellulome
• RNA-sequencing for functional prediction of RNAs
• Single cell RNA-sequencing of PBMC derived B cells from human healthy donor
• Interferon gene therapy reprograms the leukemia microenvironment inducing protective immunity to multiple tumor antigens
• Monocyte-derived IL-1 and IL-6 are differentially required for cytokine release syndrome and neurotoxicity by CAR-T cells.
• Single cell sequencing of 3 lung carcinomas
• Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - Smartseq 2 data
• Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - 10x data
• Single cell RNA-sequencing of induced Neural Plate Border Stem Cells
• Single cell RNA-sequencing of E8.5 stage embryonic neural tissue from mouse
• Single cell RNA-sequencing of primary mouse Neural Plate Border Stem Cells
• Single-cell analysis of T-cells from mouse neonate thymuses in a wild type control and a placental specific isoform of Igf2 knock-down (igf2-P0)
• Single-cell RNA sequencing of mouse germ cells
• Single-cell RNA-seq of mouse endothelial cells from three distinct embryonic locations
• Single-cell RNA sequencing of self-maintaining lamina propria macrophages
• Single-cell RNA sequencing of VE-Cadherin+ cells isolated from mouse E10.5 aorta-gonad-mesonephros region.
• Genomic encoding of transcriptional burst kinetics
• Single-cell transcriptional analysis reveals innate lymphoid cell (ILC)-like cells in zebrafish
• Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions
• Single cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells
• Single-cell transcriptional analysis reveals ILC-like cells in zebrafish
• Single-cell RNA-seq of mouse developing spinal cord
• Single-cell RNAseq of control chimeric mouse embryos at embryonic days 7.5 and 8.5 of mouse development
• Single-cell RNAseq of Tal1 knockout chimeric mouse embryos at embryonic day 8.5 of mouse development
• Single-cell RNA-seq of Pdgfra+/Sca1+/Cd31- mouse cardiac cells
• Single-cell RNA-seq of mouse cardiac interstitial cells 3 & 7 days after sham or myocardial infarction injury
• Single cell RNA sequencing of putative AIRE+ dendritic cells from human paediatric tonsillitis
• Single cell RNA-seq of mouse skin cells
• Single-cell RNA sequencing reveals a dynamic stromal niche within the evolving tumour microenvironment
• Single cell RNA seq of influenza tetramer specific CD8+ T cells from baseline
• Fibroblastic reticular cells in the spleen - total splenic Stroma cells - single cell RNAseq dataset 2

New features

• Improvements to the marker gene heatmap which displays the top 5 marker genes (sorted by p-value) grouped by cluster is available in all experiments. For instance, have a look at the heatmap in:
  • Melanoma infiltration of stromal and immune cells
  • Single cell transcriptomics of mixed asexual and sexual blood stage parasites of the rodent malaria model Plasmodium berghei
• A revised analysis pipelines which handles both SmartSeq and droplet technologies:
  • RNA-Seq alignment and quantification handled by Alevin. The alignment and quantification pipeline is written in NextFlow:
    • Droplet quantification workflow.
    • SmartSeq quantification workflow
  • Filtering and clustering handled by Scanpy. The filtering and clustering pipelines are written in Galaxy:
    • Droplet filtering and clustering
    • SmartSeq filtering and clustering

All the Galaxy tools and workflows mentioned above can be run on https://humancellatlas.usegalaxy.eu/ for reproducibility.

The Galaxy tools can be installed on other Galaxy instances through the Galaxy Toolshed. Please install the suite_scanpy_scripts and gtf2gene_list Galaxy Toolshed packages. To run the clustering part you will need 10x matrix market format files (raw normalised counts, available from the downloads on each experiment) and the GTF file for the organism in question from either Ensemble or Ensemble Genomes.

Single Cell Expression Atlas release 5 – March 2019

Data statistics

• Ensembl 95 / Ensembl Genomes 42 / WormBase ParaSite 12 gene annotations.
• This release contains 52 single cell RNA-Seq studies, consisting of 61,073 cells, of which 38,159 passed our QC from 9 different species.

New experiments

• Transcriptomic profiling of antigen-specific T cells at the single-cell level after clearance of hepatitis C virus (Human)

New features

• A marker gene heatmap which displays the top 5 marker genes (sorted by p-value) grouped by cluster is available in all experiments. For instance, have a look at the heatmap in:
  • Melanoma infiltration of stromal and immune cells
  • Single cell transcriptomics of mixed asexual and sexual blood stage parasites of the rodent malaria model Plasmodium berghei
• Tabular search results with cleaner, easier-to-discriminate, experiment details. Check out any of the following examples:
  • CFTR (gene symbol),
  • ENSG00000115904 (Ensembl ID)
  • 657 (Entrez ID)
  • MGI:98354 (MGI ID)
  • FBgn0004647 (FlyBase ID)

Single Cell Expression Atlas release 4 – November 2018

Data statistics

• Ensembl 94 / Ensembl Genomes 41 / WormBase ParaSite 11 gene annotations.
• This release contains 50 single cell RNA-Seq studies, consisting of 60,905 cells, of which 38,036 passed our QC from 9 different species.

New experiments

• Single-cell RNA-seq of mouse embryonic stem cells to study the genomic encoding of transcriptional burst kinetics (Mouse)
• Single-cell RNA-seq analysis of adult human breast epithelial cells (Human)
• Single cell sequencing of iPSC-dopamine neurons reconstructs disease progression and identifies HDAC4 as a regulator of Parkinson cell phenotypes (Human)
• Single-cell RNA-seq of de-differentiated mammary adipocytes during lactation (Mouse)
• RNA-seq of coding RNA from single cells to assess the impact of aging on cell-to-cell transcriptional variability during immune stimulation (Mouse)
• Single-cell RNA-Seq data of zebrafish blood cells (Zebrafish)
• Determining single-cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hours post fertilization (Zebrafish)

New features

• Tabular search results with cleaner, easier-to-discriminate, experiment details. Check out any of the following examples:
  • CFTR (gene symbol),
  • ENSG00000115904 (Ensembl ID)
  • 657 (Entrez ID)
  • MGI:98354 (MGI ID)
  • FBgn0004647 (FlyBase ID)

Expression Atlas release 43 – October 2025

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
  array design probe set mappings.
• This release contains 4562 datasets (161199 assays), in particular:
  • 1512 RNA-seq and 123 proteomics datasets, of which 375 report baseline gene expression, across a total of 48 different organisms;
  • 1026 datasets reporting expression in plants;
  • 4187 datasets studying samples in 14587 differential comparisons across 51 different organisms.
  • 67 overall species count

Software features

New default view for baseline experiments

All baseline experiments - both transcriptomic and proteomic - now feature a marker-gene-based view as the default display. This new interface highlights the top marker gene(s) per condition, making it easier to explore tissue- or condition-specific expression patterns.

Marker genes are identified using the Marker Gene Finder for RNA-seq (MGFR) algorithm, which assigns a specificity score to each gene based on how uniquely it is expressed. The complete marker gene lists for each experiment are available for download from our FTP.

Users can toggle between the Marker Genes and traditional expression views by selecting or deselecting the Marker Genes checkbox - for example, see RNA-seq of coding RNA from seven Bos taurus tissues.

Further details are available in our FAQ and Help pages.

Easier discovery of datasets by technology type

A new technology filter has been added to the experiment search page, making it easier to identify and browse experiments by their technology (i.e. proteomics) and improving overall discoverability.

Expression Atlas release 42 – July 2025

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
  array design probe set mappings.
• This release contains 4562 datasets (161199 assays), in particular:
  • 1512 RNA-seq and 123 proteomics datasets, of which 375 report baseline gene expression, across a total of 48 different organisms;
  • 1026 datasets reporting expression in plants;
  • 4187 datasets studying samples in 14587 differential comparisons across 51 different organisms.
  • 67 overall species count

Highlights

New species

• A new species has been added to the Bulk Expression Atlas: Dictyostelium discoideum, the first protist included. The study features RNA-Seq data of terminal differentiated cells

New plant datasets

• Total of 12 new plant datasets from sorghum, rice, Arabidopsis and maize have been added in this release, e.g Variation in gene expression between two Sorghum bicolor lines differing in innate immunity response or RNA-seq samples of ten tissues for each of the 25 genomes of the Nested Associated Mapping (NAM) maize sequencing project

New analysis in the European Diagnostic Transcriptomic Library (EDTL) collection

• Additional gene expression analysis Diagnosis of multisystem inflammatory syndrome in children (MIS-C) by a whole-blood transcriptional signature - differential analysis has been performed for data from the European Diagnostic Transcriptomic Library (EDTL) collection

New analysis data files available for download

• We have implemented a new pipeline to identify marker genes for each experimental group in baseline experiments. The analysis results are now downloadable via our FTP and will be included and visualised directly on the experiment pages in a future release. You can find more information about this data in our FAQ under the section ‘Can I get marker genes for the different experimental groups?’

Selected new experiments

Selected differential experiments

• Comparative transcriptome analysis reveals conserved defence responses in maize and sorghum to Exserohilum turcicum - maize data
• Comparative transcriptome analysis reveals conserved defence responses in maize and sorghum to Exserohilum turcicum - sorghum data
• Diagnosis of multisystem inflammatory syndrome in children (MIS-C) by a whole-blood transcriptional signature - differential analysis
• Genome-wide analysis of abscisic acid biosynthesis, catabolism, and signaling in Sorghum bicolor under saline-alkali stress
• Transcription profiling of mouse Lgr6+ epidermal stem cells in denervated or untreated skin
• Transcriptional networks identify synaptotagmin-like 3 as a regulator of cortical neuronal migration during early neurodevelopment
• Graphene Oxide Substrate Promotes Neurotrophic Factor Secretion and Survival of Human Schwann-Like Adipose Mesenchymal Stromal Cells - RNAseq
• RNA-seq comparing WT to HDAC3 and Dax1 knock-out clones in cell-sorted populations in 2iLIF and SL(RA) differentiation conditions
• RNA-seq of CN, CN/AML, and CN/AML BAALC KO iPSCs-derived HSPCs
• Transcriptomic response to ex vivo IL33 stimulation of blood eosinophils from mepolizumab- or omalizumab-treated patients
• Transcriptional changes in MCF7 cells upon ISX treatment
• RNA-Seq analysis of E15.5 mouse Insm1, Neurod1 and Pax6 knockouts vs Insm1GFP.Cre/+ controls
• All-trans retinoic reduces the levels of cardiolipins in the NB4 acute promyelocytic leukemia cell-line affecting the autophagy and differentiation responses
• Transcriptomes and differential gene expression analysis of the Arabidopsis cells that received type-III effectors delivered by Xanthomonas campestris pv. Campestris (Xcc) bacterial mutants
• RNA-seq of human oesophageal adenocarcinoma OE19 cell line following PPARGC1A knock-down and 24 hour lapatinib treatment
• Loss of full-length dystrophin expression causes major cell-autonomous abnormalities in proliferating myoblasts
• Endogenous vitamin E metabolites mediate allosteric PPARγ activation with unprecedented co-regulatory interactions
• RNA-seq of retinal organoids differentiated from hESCs carrying mutations in the RB1 gene
• Pharmacological inhibition of 17β-hydroxysteroid dehydrogenase inhibits endometrial cancer growth in an orthotopic xenograft mouse model
• Distinct Cellular Strategies Determine Sensitivity to Mild Drought of Arabidopsis Natural Accessions
• Acute effects on the human peripheral blood transcriptome of decompression sickness secondary to scuba diving
• RNA-seq of mouse lung tissue in wild type versus BMP9/BMP10 double knockout mice
• Gene expression profiling of Ercc1-/- and age-matched wt pancreata
• MiR-802 is a Tumor Suppressor of Early Stage Pancreatic Cancer
• RNA-Seq of wild type and osmtd2 mutant rice anthers
• AmpliSeq Data of WT and SLC38A10 knockout primary cortex cells in amino acid starvation and refed conditions
• Suppression of HSF1 activity by wildtype p53 creates a driving force for p53 loss-of-heterozygosity
• Time series RNA-seq of Th1 differentiation: The effect of Progesterone on Th1 differentiation?
• RNA-Seq of wild type and tape-1 mutant rice anthers
• RNA-seq of human intestinal organoids infected with Salmonella enterica at 2.5h and 8h post infection
• RNA-seq of small intestinal organoids treated with IL-13 for 0, 1, 4 8 and 24 hours and with the BMP signaling inhibitor DMH1
• RNA-Seq of human fibroblasts exposed to X-ray radiation
• Gene expression profiling (RNA-seq) experiment where CRISPRi guides were designed to target the human rs2650492 variant, the promoter of GAPDH, and a non-coding region near TUFM in HEK293t cells
• RNAseq of Huh7 and Huh7.5 cells treated with interferon alpha, beta or lambda.
• Ablation of Lgr5-positive cells in intestinal polyps from ApcMin;Lgr5DTR mice
• Kidney RNAseq data from adult F344 and Hsd11b2 knockout rats (Model of SAME)
• RNA-seq of LSK isolated from Zrsr2 mutant, Tet2 mutant and Zrsr2/Tet2 double mutant against wild-type controls
• Identification of A Blood-based 9-hub-gene Signature for Metabolic Syndrome by Machine Learning Algorithms and Integrated Bioinformatics Analysis
• RNAseq of 6 genome edited human RPE1 cell lines (compared to the parental control) disrupting the MIA3 gene.
• RNA-seq of mouse neutrophils polarized to proinflammatory N1 by lipopolysaccharide and interferon-γ or anti-inflammatory N2 by interleukin-4 versus control
• RNA-seq of WT vs isw1 delta S. cerevisiae cells during Unfolded Protein Response time course
• RNA sequencing of WT and Zeb1200M islets
• RNA-seq experiment of mouse embryonic stem cells (mESCs), comparing TCF/LEF quadruple knock-out cells with wild type cells
• A transcriptome analysis study with the focus on the role of long non-coding RNAs in Down syndrome subjects
• RNA-Seq of the murine hypothalamic cell line mHypoA-2/10 after glucose stimulation
• RNA-seq of human MDS/AML cell line OCI-M2 treated with 5-azacytidine and sulforaphane
• RNA-Seq of WT Flp-In T-REx 293 and UPF3B knockout cell lines with additional siRNA-mediated control or UPF3A knockdowns
• RNA-seq of human ES cell lines HUES4 and H1, differentiated for 5 or 7 days towards pancreatic endoderm
• RNA-Seq of WT Flp-In T-REx 293, UPF3B knockout and UPF3A-UPF3B double knockout cell lines with additional siRNA-mediated control or UPF3B knockdowns
• RNA-Seq of WT Flp-In T-REx 293, UPF3A knockout and UPF3A overexpression cell lines in part with additional siRNA-mediated control or UPF3B knockdowns
• RNA-seq of bone marrow neutrophils from wild-type mice (C57BL/6) and CD40LG knockout mice.
• RNA-seq in Arabidopsis thaliana Col and hcr2 mutant
• Ladostigil attenuates the oxidative and ER stress in human neuroblast-like SH-SY5Y cells
• DOCK1 gene derived hsa_circ_0020397 RNA is over-expressed in luminal mammary tumors and it is involved in the epithelial differentiation, growth and motility of the neoplastic cell
• RNA-seq from WT and HSALR (a Myotonic Dystrophy type 1 model) mice
• RNAseq of wild type Col-0 Arabidopsis plants and piezo/feronia/camta3 mutants before and 22 minutes after touch treatment
• LPS response of cardiovascular endothelial cells transduced with an APEX1(1-20) expressing vector or an empty vector
• Nfkb2 deficiency and its impact on the murine small intestinal mucosa
• RNA-seq of wildtype and JADE1/2/3 knockout mIMCD3 kidney cells
• Heart RNA-seq of control mice and mice with titin PEVK domain knockout, Rbm20 RNA recognition motif knockout, or double knockout
• RNA-seq to investigate the FBXO38 knockout in mouse Sertoli cells
• RNA-seq data of rs2280381-containing region knock out clone in U-937 cell line
• Deficiency of ERO1 and activation of protein translation synergistically impair breast tumor resilience
• RNA-seq of mouse brain tissue after exposure to p-cresol glucuronide
• ROBO3s: a novel ROBO3 shot isoform promoting breast cancer aggressiveness
• Aortic valve transcriptome in CHIP, non-CHIP and non-calcific controls.
• Sodium accumulation and blood capillary rarefaction in the skin predispose spontaneously hypertensive rats to salt sensitive hypertension.
• The impact of chemerin on transcriptomic profile of swine luteal cells during mid-luteal phase of estrous cycle
• A shared gene expression signature in human blastocyst embryos affected by a mitochondrial defect.
• Nobiletin ameliorates high fat-induced disruptions in rhythmic glucagon-like peptide-1 secretion - primary L cells
• RNA-seq of mouse intestinal organoids treated with interferon-gamma
• RNA-seq of mouse intestinal organoids treated with TGF-beta
• An in vitro effect of PPAR beta/delta ligands on transcriptomic profile of porcine corpus luteum during LPS-induced inflammation

Selected baseline experiments

• RNA-Seq data of terminal differentiated cells in Dictyostelium discoideum
• Variation in gene expression between two Sorghum bicolor lines differing in innate immunity response
• Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum.
• Characterization of growth and development of sorghum genotypes with differential susceptibility to Striga hermonthica

Expression Atlas release 41 – November 2024

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
  array design probe set mappings.
• This release contains 4476 datasets (159469 assays), in particular:
  • 1428 RNA-seq and 123 proteomics datasets, of which 371 report baseline gene expression, across a total of 47 different organisms;
  • 1014 datasets reporting expression in plants;
  • 4105 datasets studying samples in 14363 differential comparisons across 51 different organisms.
  • 66 overall species count

Selected new experiments

Highlights

• A new experiment, Diagnosis of multisystem inflammatory syndrome in children (MIS-C) by a whole-blood transcriptional signature, which includes data arising from the DIAMONDS project has been loaded and added to the European Diagnostic Transcriptomic Library (EDTL) collection
• 15 new human proteomics datasets have been added in this release - e.g. Proteomic characterization of human hepatocellular carcinoma (HCC) tumor biopsies, connected to this publication (preprint): Integrated View of Baseline Protein Expression in Human Tissues using public Data Independent Acquisition datasets
• RNA-seq samples of ten tissues for each of the 25 genomes of the Nested Associated Mapping (NAM) maize sequencing project

Selected differential experiments

• Global gene expression in the adult Gata6 null mouse pancreas
• RNA-seq of mouse colon to investigate how suppression of HSF1 activity by wildtype p53 creates a driving force for p53 loss-of-heterozygosity
• Ampliseq transcriptomic array of REF seq. genes in ZEB1 knock out triple negative breast cancer cells
• Ampliseq transcriptomic array of REF seq. genes in Snai1 knock out triple negative breast cancer cells
• RNA-seq of human ovarian cancer cell line SKOV3 treated with BMP2 against untreated controls
• Saccharomyces cerevisiae transcriptome response to overexpression of the Phytophthora sojae Avh110 effector
• RNA-seq of WT and dja6 dja5 mutant in Arabidopsis thaliana
• RNA-Seq of Oryza sativa Dongjin (rice) wild type and gori mutant anthers

Selected baseline experiments

• Diagnosis of multisystem inflammatory syndrome in children (MIS-C) by a whole-blood transcriptional signature
• RNA-seq samples of ten tissues for each of the 25 genomes of the Nested Associated Mapping (NAM) maize sequencing project
• Evaluation of iTRAQ and SWATH-MS for the quantification of proteins associated with insulin resistance in human duodenal biopsy samples
• Impact of ultrastructural left-ventricular Ca2+ release unit remodeling in hemodynamic subtypes of severe aortic stenosis
• DIA-MS analysis of 21 breast cancer tissues
• The muscle proteome reflects changes in mitochondrial function
• The dataset to discover ESCC related proteins
• Atopic dermatitis epidermis PCT-DIA
• Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression
• Proteomics of thyroid tumours - Proteomics of thyroid tumours provides new insights into their molecular composition and changes associated with malignancy
• GENETIC SUBTYPE- AND CELL TYPE-SPECIFIC PROTEIN SIGNATURES IN FRONTOTEMPORAL DEMENTIA
• Proteomics of the dentate gyrus reveals semantic dementia specific molecular pathology
• Distinct cell type-specific protein signatures in GRN and MAPT genetic subtypes of frontotemporal dementia
• Comparison of Lung Cancer Proteome Profiles 3: DIA
• Proteomic characterization of human hepatocellular carcinoma (HCC) tumor biopsies
• The proteome of hand eczema assessed by tape stripping
• Identification of carcinogenesis and tumor progression processes in pancreatic ductal adenocarcinoma using high-throughput proteomics

Expression Atlas release 40 – May 2024

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
  array design probe set mappings.
• This release contains 4451 datasets (157607 assays), in particular:
  • 1418 RNA-seq and 108 proteomics datasets, of which 354 report baseline gene expression, across a total of 47 different organisms;
  • 1011 datasets reporting expression in plants;
  • 4097 datasets studying samples in 14354 differential comparisons across 51 different organisms.
  • 66 overall species count

Software features

• New cross-links have been added between related transcriptomics and proteomics experiments to better support data integration across the two modalities - e.g. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

Selected new experiments

Highlights

• Latest GTEX version has been added to Expression Atlas Genotype-Tissue Expression (GTEx) featured experiment updated to V8, the most current release for bulk tissue expression
• 15 new proteomics datasets have been added in this release:
• 14 pig proteomics experiments - e.g. Annotation of the domestic pig genome by quantitative proteomics
• 1 Arabidopsis proteomics experiment Arabidopsis proteomic tissue atlas

Selected differential experiments

• Time course RNA-seq analysis of barley MLA1 immune receptor-mediated response to barley powdery mildew fungus Bgh in defense phytohormone signaling-depleted Arabidopsis thaliana mutant.
• RNA-seq analysis of MCT8-deficient and healthy control brain microvascular endothelial cells (BMECs) and neural cells
• RNA-seq to investigate Auxin responsive genes in the Arabidopsis stem
• RNA-seq of Control and SMRT KD CD8α+ DCs at 0hr and 6hr CpG stimulation
• RNA-seq of hESCs undergoing primed to naive-like resetting via exogenous KLF17 overexpression
• RNA-sequence to compare the transcriptional profiles of nuclear and plastidic genes in the atnusg and the wild-type
• RNA-seq of hESCs overexpressing inducible KLF17 versus uninduced controls.
• Reactive astrocytes transduce blood-brain barrier inflammation through a TNFα-STAT3 signaling axis and secretion of alpha 1-antichymotrypsin
• Axon Guidance Receptor ROBO3 Modulates Subtype Identity and Prognosis via AXL-associated Inflammatory Network in Pancreatic Cancer
• Effects of innate immune stimuli on PAF1 knockout cells
• RNAseq of whole ovarian follicles from young and old mice.
• RNA sequencing of primary isolated unstimulated murine splenic DC1 and DC2 from specific pathogen free (SPF), Germ free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice
• Influence of CAP-D3 in Arabidopsis thaliana transcription

Selected baseline experiments

• The Genotype-Tissue Expression (GTEx) project v8
• RNA-seq of coding RNA from tissue samples of 122 human individuals representing 32 different tissues
• Proteomics characterization of human colon and rectal cancer
• A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
• Holistic proteome analyses of heart samples from GHR-deficient (GHR-KO) pigs
• Proteomic analysis of liver tissue from a WT pig
• Proteomic changes of the liver in the absence of growth hormone (GH) actions
• Branch retinal vein occlusion in a porcine model
• Comparison of two solid-phase extraction (SPE) methods for the identification and quantification of porcine retinal protein markers by LC MS/MS
• Annotation of the domestic pig genome by quantitative proteomics
• Proteomic analysis of pig adipose tissues
• Analysis of skeletal muscle from a tailored pig model of Duchenne muscular dystrophy
• Proteome analysis of skeletal muscle samples from a porcine model of Duchenne muscular dystrophy treated by somatic gene editing
• Proteome analysis of skeletal muscle samples from a porcine model of Duchenne muscular dystrophy
• Bacterial and host proteins along and across the porcine gastrointestinal tract
• The protein expression landscape of the heart across humans and model organisms
• Proteomics of pig heart and skeletal muscle tissue
• Getting to the heart of the matter: Multispecies heart tissue proteome characterization
• Arabidopsis proteomic tissue atlas

Expression Atlas release 39 – July 2023

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
  array design probe set mappings.
• This release contains 4424 datasets (158401 assays), in particular:
  • 1406 RNA-seq and 93 proteomics datasets, of which 340 report baseline gene expression, across a total of 47 different organisms;
  • 1007 datasets reporting expression in plants;
  • 4084 datasets studying samples in 14283 differential comparisons across 51 different organisms.
  • 66 overall species count

Selected new experiments

New species!

• Drosophila pseudoobscura

New featured collection! - with data arising from the DIAMONDS project

• European Diagnostic Transcriptomic Library (EDTL)

Selected differential experiments

• Molecular Response of Chorioretinal Endothelial Cells to Complement Injury: Implications for Macular Degeneration
• Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for Wild Type and Mutants including opaque2, PbfRNAi and PbfRNAi;o2 in Maize (Zea mays)
• RNA-seq to investigate dual role of lesion simulating disease 1 as a condition-dependent scaffold protein and transcription regulator in Arabidopsis thaliana
• Germinal Center B-Cell gene expression comparison between Wiskott-Aldrich syndrome protein KO mice and WT mice
• RNA-Seq of zebrafish whole-eye comparing wild-type and mab21l1 c.107delA p.(Lys36Argfs*7) embryos at 5 days post fertilization
• RNA-seq of mouse embryonic fibroblasts(MEFs) with knock-out of SERF2 compared to control MEFs
• RNA-seq: STAT1 and STAT3 transcription factors sense and interpret changes in inflammation through engagement of specific enhancers
• Mutant FUS triggers age-dependent synaptic impairment in presymptomatic ALS-FUS mice (RNA-seq part2)
• RNA-Seq analysis of the Oryza sativa Dongjin wild type and far1-1 mutant anthers
• RNA-seq to investigate gene expression after HCV eradication with IFN therapy in HIV/HCV-coinfected patients
• RNA-seq of oocytes and zygotes from pabpn1l ko and wt female mice
• Intestinal ulcers from biopsy-wounded wild-type and Bmp4-overexpressing mice
• RNA-seq of mouse sciatic peripheral nerve of injured mouse with implant: control (untreated) vs local delivery of MCC950 (NLRP3inh) vs standard FBR treatment dexamethasone (Dex). .
• RNA-seq of human oesophageal adenocarcinoma OE19 cell line treated with lapatinib
• RNA-seq following shRNA-mediated knock-down of ETV6-RUNX1 in the B-ALL cell line Reh
• RNA-seq of C. elegans reared on experimental microbiome (EM) and EM cell-free media against OP50-fed controls
• RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)
• RNA-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR) and with or without prior TNFa treatment (IR_TNF)
• Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS and NINJA repressor proteins to reprogram plant jasmonate signaling (GUS overexpression)
• Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS and NINJA repressor proteins to reprogram plant jasmonate signaling (rolB overexpression)
• RNA-seq of definitive endoderm and pancreatic progenitor cells derived in vitro from human pluripotent stem cells in order to study the role of transcription factor GATA6 in human pancreas development
• Gene expression ATLAS of Brachypodium distachyon (cv. BD21) during photomorphogenesis (transition from dark to light)
• Transcriptome analysis of HSPC, THP1 and K562 cells under IFNɑ treatment
• RNA-seq of PBMC derived macrophages derived from healthy donors in response to lipid A or TNF alpha (Dataset_170630_SysmedIBD_RNA_HEngland)
• RNA sequencing analysis for differentially expressed genes in neonatal rat cardiomyocytes following knockdown of transcription factor Vezf1
• RNA-seq analysis of C. elegans mina-1 mutants
• RNA-seq from cortex and hippocampus of mice harboring heterozygous and homozygous deletion of Kctd13, as well as wild-type controls.
• Comprehensive RNA-Seq Profiling of the Lung Transcriptome of Bashbay Sheep in Response to Experimental Mycoplasma ovipneumoniae Infection
• RNA-seq of Drosophila melanogaster testes upon knock-down of dCoREST, dLSD1 and controls
• RNAseq of proneural glioblastoma stem-like cells 72 hours after infection with human cytomegalovirus (CMV) Towne strain
• RNA-seq analysis of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants, profiled at different time points after leaf appearance and with different watering conditions
• Pro-inflammatory cytokines drive functional deregulation of potassium channels in primary synovial fibroblasts
• RNASeq of human mesenchymal stem cells (6 donors) with and without treatment with 1 hour of cyclic tensile strain (2.6 – 6.2% strain, 5.0 Hz).
• An integrated approach to profile lung tumor endothelial cell heterogeneity across species and models and to identify angiogenic candidates
• Thyroid deficiency before birth modifies adipose transcriptome to promote overgrowth of white adipose tissue and impair thermogenic capacity
• RNA-Seq profiling of ERCC1-XPF DNA repair defect (Er1F/-) versus wild type (Er1F/+) macrophages
• RNA-Seq of SOX4 and HOXD3 CRISPR KO SupT1 cells against wildtype SupT1 cells during HIV-1 infection
• Transcriptomic analysis of cocoa (Theobroma cacao L.) response to water deficit.
• RNA-seq of RS4:11 cell line populations that are unedited (SPI1 +/+), mono (SPI1 +/-) and biallelicaly edited (SPI1 -/-)
• RNA-seq of blood samples from patients diagnosed with visceral leishmaniasis and asymptomatic individuals (Brazil)
• RNA-seq of whole tissue of 3 days post fertilization atp6v1e1b-deficient zebrafish larvae and wild-type controls
• A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth
• RNA-Seq of BEAS-2B cells treated with low doses of Ni and NiO nanoparticles as well as NiCl2 for 6 weeks
• Zebrafish il-4 il-10 regulated immunity in gills
• RNA-seq experiment of developing mouse forelimbs, comparing Bcl9/9l mutant with control littermates.
• RNA-Seq of wild type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate (DSS)
• RNA-seq of wild type and mutant Drosophila flies with a deletion of the gene CG16717 (dMPPED)
• RNA-seq of sfpq-/- zebrafish embryos and siblings at 24 hpf
• RNA-Seq of transgenic rice (Oryza sativa spp. japonica cultivar Kitaake) plants containing a single construct that over-expresses C4 metabolic pathway components CA, PEPC, MDH, ME and PPDK
• RNAseq of small intestinal organoids from mice treated with the cytokines IFNG, IL-13 and IL-22 for 24 hours
• RNAseq of small intestinal epithelium extracted from mice infected with Nippostrongylus brasiliensis
• RNAseq of colon intestinal epithelium extracted from mice infected with Citrobacter rodentium
• RNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle
• RNA-Seq of Arabidopsis thaliana plants primed by insect eggs from Pieris brassicae and triggered by insect herbivory against untreated controls in two different developmental phases (vegetative vs. reproductive)
• Role of Macrophage migration inhibitory factor (MIF) in pancreatic stellate cells (PSCs)
• RNA-seq of Zbtb10 Knockdown and Control cDC1 dendritic cells (Cd8+)
• Transcriptome analysis in the old Brazilian wheat variety Toropi in response to infection with Puccinia triticina, the causal pathogen of leaf rust
• mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups
• mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups
• RNA sequencing of GPRC5C-Knockdown (GPRC5C-KD) and control CD34+ human bone marrow
• RNA sequencing of control and GPRC5C-Overexpression (GPRC5C-OE) in human mobilized peripheral blood (mPB)
• 3’ mRNA-seq of sfpq-/- zebrafish embryos and siblings at 24 hpf
• RNA-seq profiling of three distinct cell populations in a murine model of epilepsia with and without drug treatment
• Influence of SUMOylation on transcriptional signature of hIPSCs (ChiPS4) assessed by time-resolved RNA-seq in response to ML792 treatment
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with A.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with B.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with F to I.
• Profiling of human bronchial epithelial BEAS-2B infected with influenza A and treated with succinate to study the anti-influenza activity of succinate
• Transcriptomic analysis investigating the role of TNC in tumor progression using the MMTV-NeuNT mouse model
• Microarray analysis of MRC-5 cells infected with Zika virus strains
• Transcriptional profiling by array of U2OS cells overexpressing the BRCT domain of PARP1 after UV radiation
• Neurog3-independant role of Notch signaling in pancreas explants. Microarray of pancreata of Wildtype or Neurog3tTA/tTA (Neurog3-Null) background at E12.5, explanted for 3d + treatment 24h with DAPT/vehicle.
• Expression profiles of Hif1a mutant and wild type mouse livers subjected to cycles of fasting and re-feeding
• Transcriptomic analyses of 11.5 dpc female germ cell (mouse) exposed or not to Bisphenol A analogues (BPAF and BADGE)

Selected baseline experiments

• RNA-seq from gastrocnemius muscles from rats aged 6
• RNA-seq from tibialis muscles from rats aged 15 months (adult) and 27 months (old)
• RNA-seq of Zbtb20-expressing Tregs against activated (CD62Llo) and naive (CD62Lhi) Tregs that do not express Zbtb20
• RNA-seq analysis of quiescent human splenic B cell populations
• Global gene expression differences between blood- and lymphatic-specific human dermal microvascular endothelial cells
• A genetic
• Temporal analysis of mRNA from panicle tissue from field grown rice
• Transcriptome dynamics during the onset of conceptus elongation and between female and male porcine embryos
• RNA-Sequencing of whole blood samples from children with a range of acute febrile illnesses
• Genome-wide expression profiling and phenotypic evaluation of European maize inbreds at seedling stage in response to heat stress
• RNA-Seq of hippocampus in Diversity Outbred mice
• Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice
• The role of cis regulatory evolution in Zea Mays domestication
• RNA-seq data of Arabidopsis thaliana germination
• RNA-seq of human neuroblastoma cell lines
• Genome-wide gene expression profile in inner stem tissue of V2 seedlings and husks (maize B73) [RNA-Seq]
• Transcriptional analysis of tendons from rat
• Gene expression in B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination
• Transcript profile analyses of maize silk strands during silk senescence
• Distinct small RNA populations act antagonistically in formation of heterosis
• RNA-Seq of various rice tissues (Root hair
• RNAseq of murine brown fat
• modENCODE: RNA-seq of gonads and carcasses in Drosophila pseudoobscura
• RNA-Seq of cultivated (i) bulk human thymic epithelial cells (hTECs) (ii) cortical hTECs (iii) medullary hTECs (iv) human thymic interstitial cells (hTICs)
• Transcriptome profiling of various organs at different developmental stages in rice (single-end)
• Transcriptome profiling of various organs at different developmental stages in rice (paired-end)
• RNA-sequencing of maize tissues at different developmental stages (comparative transcriptome study)
• High-resolution gene expression datasets of ontogenetic zones in the root apical meristem\

New proteomics experiments

• Secretome analysis of colorectal cancer cell linesSW620
• Proteomics of whole cell lysate vs. extracellular vesicles
• Proteome analysis of formalin-fixed paraffin-embedded colorectal adenomas
• Biomarkers discovery for Colorectal cancer liver metastasis
• Biomarkers discovery for Colorectal cancer
• Tissue-exudative extracellular vesicles of colorectal cancer
• Identification and validation of stage-associated serum biomarkers in colorectal cancer stages.
• Quantitative proteomics analysis of paired colorectal cancer and non-tumorigenic tissues
• Global proteome analysis of paired colorectal cancer sample using LC-MS/MS
• Proteome Landscapes of the Human Colorectal Mucosa
• Molecular composition of serum exosomes

Expression Atlas release 38 – February 2022

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
  array design probe set mappings.
• This release contains 4,315 datasets (153,212 assays), in particular:
  • 1,314 RNA-seq and 83 proteomics datasets, of which 301 report baseline gene expression, across a total of 46 different organisms;
  • 982 datasets reporting expression in plants;
  • 4,012 datasets studying samples in 13,788 differential comparisons across 51 different organisms.
  • 65 overall species count

Software features

• More supplementary files for proteomics experiments are available for downloads, including:
  • the unprocessed raw output file (proteinGroups.txt), which contains the output from MaxQuant before processing and submission into Expression Atlas.
  • the parameter file (mqpar.xml), which has all input parameters used to run MaxQuant for each study.
• New proteomics differential and proteomics baseline (SWATH-DIA) experiment types are added.
  • Example (Proteomics differential): https://www.ebi.ac.uk/gxa/experiments/E-PROT-39/Results
  • Example (Proteomics baseline DIA): https://www.ebi.ac.uk/gxa/experiments/E-PROT-66/Results
• Improved error messages that are more informative for the user.
• Improved performance in queries for expression heatmaps, which should user wait and errors.
• Improved file download.

Selected new experiments

Selected differential experiments

• The dicerlike1 homologue, fuzzy tassel, is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize
• RNA-seq of SARS-CoV-2 infected lungs from mice sensitized for SARS-CoV-2 infection by Ad5-hACE2 transduction compared to non-sensitized mice
• RNA-seq of SH-SY5Y NB cells stably transduced with shETV5 compared to parental cells
• RNA sequencing of corticospinal neurons and control callosal projection neurons purified from the cerebral cortex of adult wild-type and Sod1G86R mice
• Human cortical organoids. Chronic treatment with GSK3 inhibitor CHIR99021. Bulk RNAseq.
• Redox activation of excitatory pathways in auditory neurons as mechanism of age-related hearing loss
• RNA-Seq of myeloid derived suppressor cells (MDSCs) from wild-type and Rel knockout mice
• RNA-seq of a time course of spinal cord regeneration following tail amputation in Xenopus tropicalis tadpoles at stage 50
• RNA-Seq of enteroids from wild-type and Tnfaip8 knockout mice.
• RNA-seq of doxycycline induced tumor and residual mouse primary mammary epithelial cells grown in 3D cell cultures against non-induced controls
• Gene expression changes in the cerebellum, cortex and spinal cord of MATR3 S85C knock-in mice at pre-symptomatic stage 8-10 weeks of age
• The effect of very-high-molecular-mass hyaluronan (vHMM-HA) on CD44-overexpressing IMR90 cells
• Transcriptomic analysis of the distal colon of wild type C57BL/6N mice and mice harboring a mutation (S839I) in Gucy2c
• RNA-Seq of bone marrow derived macophages (BMDMs) and brain tissue isolated from wild type and Irgm1 knockout mice
• RNAseq of mouse embryonic fibroblasts from conditional knock-in mice carrying a phosphorylation-deficient S180A (SA) mutation in exon 5 of the endogenous mouse Trp53 gene locus
• RNA-seq of intestinal crypts vs intestinal smooth muscle with a specific MMP17 deletion compared to wild-type
• BT549 cells depleted of ELP3 compared to control
• RNA-Seq of pancreatic islets from whole body knockout of lncRNA Pax6os1 mice
• Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease
• RNA-seq analysis of crypt samples isolated from the small intestine of Bach2 KO and control mice
• Transcription profiling by array of human HhAntag-treated pancreatic xenograft tumors
• Transcription profiling by array of human HhAntag-treated pancreatic xenograft tumors
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with A.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compound starting with B.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with D to E.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with J to M.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with N to O.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with P to R.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with S to T.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies: compounds starting with U to Z.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with C.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with D and E.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with F to I.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with J to M.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with N to O.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with P to R.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with S to T.
• Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies: compounds starting with U to Z.
• RNA-seq of mouse colon to investigate how influenza infection leads to intestinal disorders
• Array results for differential gene expression in 661W
• Time Series gene expression profiling of Lethal Giant Larvae tumours in developing wings of Drosophila larvae
• Repression of OSMR and FGFR1 by miR-1/133a prevents adult cardiomyocyte dedifferentiation and cell cycle entry in the adult heart
• Acclimation of photosynthesis to changes in the environment results decreases oxidative stress in Arabidopsis thaliana
• Transcription profiling by array of post-mortem brain cortex from healthy control patients and amyotrophic lateral sclerosis (ALS) patients that carry an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 (C9ORF72) gene
• Gene Expression underlying Osteo-, Adipo-, and Chondro-Genic Lineage Commitment of Human Mesenchymal Stem Cells
• Transcriptomic response of Saccharomyces cerevisiae to imatinib
• SWATH analysis of human kidney tissues to generate a digital map representing the proteome of biopsy level clinical samples.
• 113 DLBCL SWATH maps by PCT-SWATH
• Comparison of FFPE and fresh frozen prostate tissues using PCT SWATH

Selected baseline experiments

• Proteomic and transcriptional profiling of rat amygdala following social play
• An atlas of the ageing lung mapped by single-cell transcriptomics and deep tissue proteomics
• Sex differences in the molecular signature of the developing mouse hippocampus
• Proteome changes during mouse brain ageing
• Circadian Mouse Articular Cartilage Proteomics
• Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics
• Proteomics analysis of rat liver from the disulfiram treatment
• Rat testis LC-MS/MS - Integrated proteomics and metabolomics analysis of rat testis
• A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression
• The Comprehensive Mouse Retina Proteome
• Protein expression in the dorsolateral prefrontal cortex of normal
• Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix
• Proteomic analysis of microdissected renal tubules
• Quantitative proteomics profiling determines the uniqueness of the sinus node
• Quantitative proteomics of human heart samples collected in vivo reveal the remodeled protein landscape of dilated left atrium without atrial fibrillation.
• The protein expression landscape of the heart across humans and model organisms
• Proteomic evaluation of decellularized human umbilical artery
• Proteomic Atlas of the Human Brain in Alzheimer’s Disease
• Proteomic Investigation of EVLP Tissue Lung Lobes
• Proteomic comparison study between the female and male tendon
• Influence of spermidine on the mouse brain proteome
• Heterogeneity of proteome dynamics between connective tissue phases of tendon in adult rats
• Vinculin-network mediated cytoskeletal remodeling regulates contractile function in the aging heart
• Myocardial proteome from obese rats with cardiac dysfunction C4PR_LIV
• Proteomic analysis of the spatiotemporal based molecular kinetics of acute spinal cord injury identifies a time- and segment-specific window for effective tissue repair
• Proteome-transcriptome analysis and proteome remodelling in mouse lens epithelium and fibres
• Label-Free Absolute Protein Quantification with Data-Independent Acquisition
• OLFM4 expression in breast tumor samples
• NCI60 proteome by PCT-SWATH - Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines
• 76 human liver tissue proteomes by PCT-SWATH
• Quantification of Proteome heterogeneity in benign and malignant prostate tissues
• PCP39: prostate cancer proteome for 39 patients by PCT-SWATH
• Quantitative variability of 342 plasma proteins in a human twin population

Expression Atlas release 37 – March 2021

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations.
  array design probe set mappings.
• This release contains 4169 datasets (139128 assays), in particular:
  • 1239 RNA-seq and 46 proteomics datasets, of which 266 report baseline gene expression, across a total of 45 different organisms;
  • 972 datasets reporting expression in plants;
  • 3903 datasets studying samples in 11692 differential comparisons across 50 different organisms.
  • 65 overall species count

Selected new experiments

Selected differential experiments - COVID-19 focus

• Lung and colon transcriptome profiling of fatal COVID-19 cases
• Spectrum of Viral Load and Host Response Seen in Autopsies of SARS-CoV-2 Infected Lungs
• Primary Human Airway Epithelial Cultures infected with SARS-CoV-2
• RNA-seq of mouse alveolar macrophages from control and Influenza A virus infected animals
• Temporal dynamics of the host molecular responses underlying severe COVID-19 progression and disease resolution

Selected baseline experiments

• RNAseq analysis on mature leaf tissue of 60 individual B104 maize inbred plants grown in the field
• RNA-seq of circadian timeseries sampling (LL2-3) of 13-14 day old Arabidopsis thaliana Col-0 (24 h to 68 h
• Mouse interscapular brown
• A 3D molecular atlas of the chick embryonic heart
• RNA-Seq of maize inbred lines and their F1 reciprocal hybrids

Selected proteomics experiments

• Region and cell-type resolved quantitative proteomic map of the human heart.
• Protein expression in the dorsolateral prefrontal cortex of normal brain samples from the Johns Hopkins and Baltimore Coroner Aging Arm of Consensus Brain Proteomics Study
• Protein expression in precuneus cortex brain samples from the Baltimore Longitudinal Study of Aging (BLSA)
• Protein expression in the dorsolateral prefrontal cortex brain samples from the Baltimore Longitudinal Study of Aging (BLSA)
• Proteome analysis of the drosolateral prefrontal cortex of human brain from Adult Changes in Thought Study collection.
• Protein expression in the temporal cortex brain samples of normal
• Protein expression in the dorsolateral prefrontal complex brain samples from the University of Pennsylvania School of Medicine Brain Bank.
• Mass spectrometry proteomics of control normal breast tissue samples
• Proteome profiling of breast cancer biopsies reveals a wound healing signature of cancer-associated fibroblasts - tumor-distant tissue sections
• Proteomic Investigations of Autism Brain
• Human colon biopsies (healthy and Ulcerative Colitis) LC-MS/MS
• Comparative proteome stability analysis of snap frozen
• Proteome of the Human Corpus Callosum and Anterior Temporal Lobe
• Individual variability of protein expression in human tissues
• Characterization of human pineal gland proteome
• Proteomic analysis of human anterior pituitary gland
• Allele-Specific Protein Abundance in Human Brain
• Brain ureido degenerative protein modifications in Alzheimer’s disease with cerebrovascular disease
• The Mount Sinai cohort of large-scale proteomic data in Alzheimer’s disease####Selecteb

Expression Atlas release 36 – August 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations and array design probe set mappings.
• This release contains 4,029 datasets (134,307 assays), in particular:
  • 1,153 RNA-seq and 25 proteomics datasets, of which 227 report baseline gene expression, across a total of 45 different organisms;
  • 941 datasets reporting expression in plants;
  • 3,802 datasets studying samples in 11,411 differential comparisons across 50 different organisms.
  • 65 overall species count

New experiments

• New Differential experiments
  • Gene expression between dry and imbibed seeds in vitamin C defective (vtc) mutants and wild-type Arabidopsis thaliana
  • RNA-seq of Arabidopsis of five-day-old wild type and abi4-1 seedlings
  • Transcription profiling of molecular phenotypes of acute kidney injury in kidney transplants
  • Transcription profiling of peripheral blood mononuclear cells from multiple sclerosis patients at baseline and after 3, 12 and 24 months of IFN-beta treatment
  • Transcription profiling of human peripheral blood mononuclear cells in vitro from CIS patients after Interferon beta-1a treatment
  • Expression data from Ribonuclease Inhibitor (RI/Rnh1) deficient Human K562 cells
  • RNA-seq of human cardiovascular endothelial cell line HUVEC, treated with different media
  • Expression data from human liver with or without type 2 diabetes
  • Expression data from colonic biopsy samples of infliximab treated ulcerative colitis patients
  • mRNA-seq of HCT116 RNF40 knockdown cells upon TNF-alpha stimulation
  • Transcription profiling of peripheral blood mononuclear cells from multiple sclerosis patients at baseline and after 3, 12 and 24 months of IFN-beta treatment
  • Expression data from Ribonuclease Inhibitor (RI/Rnh1) deficient Human K562 cells
  • Microarray analysis of islets of Langerhans from 3 week-old NOD, NOR and C57Bl/6 mice
  • RNA-seq of brown and white mouse adipose tissue at thermoneutrality and high-fat diet
  • Assessing concordance of drug-induced transcriptional response in rodent liver and cultured hepatocytes
  • RNA-seq of etiolated 9 day old maize seedling second leaves after exposure to either blue, red or no light conditions for three hours
• New Baseline experiments
  • Arabidopsis tissue atlas
  • Genome-wide transcriptome sequencing at different stages of Drosophila melanogaster development, RNA-seq
  • Variation in RNA expression in a panel of 30 breast cancer cell lines
  • Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
  • HipSci Project - RNAseq of healthy volunteers
  • Whole-transcriptome of the liver in 15-day-old C3H/HeOuJ and CAST/EiJ mice.
  • RNA-sequencing of Sorghum tissues at different developmental stages (comparative transcriptome study)
  • Transcription profiling by high throughput sequencing of Sorghum flag leaf tissue and emerging panicle tissue at panicle emergence
  • RNAseq profiling of C4 grass Sorghum bicolor bundle sheath and mesophyll cells
  • Transcription profiling by high throughput sequencing of berries from grapevine cultivar Tannat
  • Transcriptome investigations supports the role of rootstock-scion interaction in grapevine berry quality
  • RNA-seq of seven Vitis vinifera cultivar berry skin transcriptomes: Cabernet Franc, Cabernet Sauvignon, Chardonnay, Merlot, Pinot Noir, Sauvignon Blanc, and Semillon
  • RNA-seq samples of ten tissues for B73 abnormal 10 (B73_Ab10)
  • RNA-seq samples of ten tissues from Zea mays subsp. mays B73

Expression Atlas release 35 – May 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations and array design probe set mappings.
• This release contains 3,942 datasets (131,311 assays), in particular:
  • 1,091 RNA-seq and 25 proteomics datasets, of which 214 report baseline gene expression, across a total of 44 different organisms;
  • 923 datasets reporting expression in plants;
  • 3,728 datasets studying samples in 11,205 differential comparisons across 50 different organisms.
  • 65 overall species count

New experiments

• 23 experiments relevant to the research of the current COVID-19 outbreak caused by the coronavirus SARS-Cov-2.
  • Transcriptional response of human lung epithelial cells to SARS-CoV-2 infection.
  • Transcription profiling by array of human bronchial epithelial cells after infection with SARS-CoV and DOHV
  • SHAE004: SARS-CoV, SARS-dORF6 and SARS-BatSRBD infection of HAE cultures.
  • Host responses contributing to the attenuation of severe acute respiratory syndrome coronaviruses missing E protein domains
  • Transcription profiling of human bronchial epithelial cell line Calu-3 2B4 infected with Human Coronavirus MERS-CoV-London
  • SARS infection of C57BL6, TIMP1 and Serpine1 knock-out mice
  • Human airway epithelial responses to rhinovirus infection and cigarette smoke extract alone and in combination
  • Infection of wild type and CXCR3 knockout C57BL6/J mice with SARS MA15
  • Mouse lung tissue transcriptome response to a mouse-adapted strain of SARS-CoV in wild type C57BL6/NJ mice and TLR3-/- mice
  • SM001: SARS CoV MA15 infection of C57Bl/6 mouse model – Data from 4 viral doses at 1, 2, 4 and 7 days post infection.
  • Time course analysis of icSARS CoV Urbani or icSARS deltaORF6 infected Calu-3 2B4 bronchial epithelial cells
  • Transcriptional profile of PBMCs in patients with acute RSV or Influenza infection
  • Transcriptomic analysis of host response to mouse-adapted SARS virus in wild type, STAT1 -/-, and IFNAR1 -/- mouse genetic backgrounds
  • Expression data from primary human keratinocytes exposed to cytokines in vitro (IL-4, IL-13, IL-17A, IFN-alpha, IFN-gamma, TNF)
  • SCL006,icSARS CoV Urbani or icSARS Bat SRBD (spike receptor binding domain from the wild type strain Urbani to allow for infection of human and non-human primate cells) infections of the 2B4 clonal derivative of Calu-3 cells - Time course
  • SM019 - Infection with SARS MA15 of C57BL/6J mice and Tnfrsf1b knockout mice
  • SM020 - Infection with SARS MA15 of C57BL/6J mice and KEPI (ppp1r14c) knockouts
  • SM015 - Infection with SARS MA15 of C57BL/6J mice and Tnfrsf1a/1b knockouts
  • Transcription profiling of human bronchial epithelial cell line Calu-3 2B4 infected with Human Coronavirus EMC 2012
  • SM012 - SARS MA15 wild type, and SARS deltaORF6 mutant virus infections of C57BL6 mice - A time course
  • SM014 - SARS MA15 wild type, and SARS nsp16 mutant virus infections of C57BL6 mice - A time course
  • SM009 - SARS infection of C57BL6, and PLAT knock-out mice.
  • Genomic profiling of collaborative cross founder mouse strains infected with respiratory viruses to discover novel transcripts and infection-related strain-specific gene and isoform expression
• New Differential experiments
  • Transcriptome analysis of the effect of the hsl2 mutation in root tips
  • TMK1-mediated transcriptional auxin signaling guides differential growth in Arabidopsis thaliana
  • BLISTER safeguards the protein kinase activity of ER stress modulator IRE1A during plant growth and development in Arabidopsis thaliana
  • Plant development on ISS differs from the development on the ground and is influenced by the genetic background
  • RNA-seq of 21 sessile serrated colon adenoma/polyps, 10 hyperplastic polyps, 10 adenomas, 21 uninvolved colon and 20 control colon specimens
  • mRNA and small RNA associated with Crohn’s disease behavior [RNA-Seq]
  • Whole transcriptome sequencing of Treg with and without Mef2d, Mef2c, HDAC1, HDAC2 or Dyrk1 deletion
  • RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)
  • RNA-seq of leaf, root, and stem xylem from Western poplar (Populus trichocarpa) plants in response to drought, high salinity, heat and cold stress
  • RNA-seq sequencing to investigate the effect of ZmDWF4 on Zea mays seed development
• New Baseline experiments
  • BLUEPRINT EpiVar project: Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
  • RNA-seq of human islet pancreatic cells to identify eQTL loci
  • HipSci Project - RNAseq of healthy volunteers
  • Regulation of gene expression in macrophage immune response
  • Transcription profiling by high throughput sequencing of two Arabidopsis F6 hybrid mimic lines compared with either C24 or Ler parental lines
  • Zygotic Genome Activation Occurs Shortly After Fertilization in Zea mays
  • Characterization of imprinted genes in rice reveals regulation and imprinting conservation at some loci in plant species
  • Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G3E) on the berry transcriptome [RNA-seq]
  • mRNA-Seq of head tissue from Drosophila melanogaster
  • Transcription profiling by high throughput sequencing of maize B73, Mo17 and the SX19 inbred mapping population

Expression Atlas release 34 – March 2020

Data statistics

• Ensembl 99 / Ensembl Genomes 46 / WormBase ParaSite 14 gene annotations and array design probe set mappings.
• This release contains 3,744 datasets (122,669 assays), in particular:
  • 954 RNA-seq and 25 proteomics datasets, of which 188 report baseline gene expression, across a total of 43 different organisms;
  • 827 datasets reporting expression in plants;
  • 3,556 datasets studying samples in 10,423 differential comparisons across 48 different organisms.
  • 63 overall species count

New experiments

• RNA-seq of blood samples from bovines immunized with a multicomponent recombinant vaccine against cattle tick.
• Comparative transcriptome analysis provides molecular insights into the interaction of Beet necrotic yellow vein virus and Beet soil-borne mosaic virus with their host sugar beet
• In vivo assessment of ROS production and oxidative stress effects induced by chronic exposure to gamma radiation in C. elegans
• Effect of heat stress on developing wheat grain
• RNA-Seq of seed dormancy in red rice
• Microarray data sets of Arabidopsis rps10 mutants with RNAi-silenced expression of mitoribosomal S10 protein
• Expression analysis in brain endothelial cells of Gαq/11beKO mice to elucidate CO2-induced vasoreactivity mechanism

• RNAseq of human bone marrow mesenchymal stem cells in co-culture with endothelial cells

• New Baseline experiments
  • Mapping regulatory variation in sensory neurons using IPS lines from the HIPSCI project
  • Strand-specific RNA-seq of somite-staged pure-bred wild-type mouse embryos from the Mouse Genetics Project/ DMDD
• New Proteomics experiments
  • A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
  • A Multiregional Proteomic Survey of the Postnatal Human Brain
  • Proteomic Atlas of the Human Brain in Alzheimer Disease
  • Human brain Alzheimer’s

Expression Atlas release 33 – December 2019

Data statistics

• Ensembl 98 / Ensembl Genomes 45 / WormBase ParaSite 14 gene annotations and array design probe set mappings.
• This release contains 3,699 datasets (121,342 assays), in particular:
  • 918 RNA-seq and 25 proteomics datasets, of which 184 report baseline gene expression, across a total of 43 different organisms;
  • 819 datasets reporting expression in plants;
  • 3,515 datasets studying samples in 10,290 differential comparisons across 47 different organisms.
  • 62 overall species count

New experiments

• RNA-seq comparing transcriptome of lymphoblastic cells from FAME patients and control individuals
• RNA-seq of laser micro-dissected cartilage after surgical induction of osteoarthritis in increased ER stress mice
• PSC-IBD mucosal biology
• RNA-seq of frontal cortex in a novel mouse model of Alzheimer’s disease
• RNA-Seq of developing shoot apical meristems of barley cultivar Bonus and two allelic praematurum-c/mat-c mutants mat.c.907 (NGB 116862) and mat.c.943 (NGB 117474) grown under long- and short-day photoperiods
• RNA-Seq in midbrain of Coq9R239X mice treated with Rapamycin
• Comparative transcriptome profiling of the response to Pyrenochaeta lycopersici in resistant tomato cultivar Mogeor and its background genotype - susceptible Moneymaker

• Effect of diets supplemented with linseed alone or combined with vitamin E and selenium or with plant extracts on Longissimus thoracis transcriptome in growing-finishing Italian Large White pigs

• New Baseline experiments
  • RNA-seq of long poly adenylated RNA and long non poly adenylated RNA from ENCODE cell lines
  • Opossum RNA-seq time-series of the development of seven major organs
  • RNA-sequencing of human embryonic and fetal urinary bladder and genital tissues

Expression Atlas release 32 – September 2019

Data statistics

• Ensembl 96 / Ensembl Genomes 43 / WormBase ParaSite 12 gene annotations and array design probe set mappings.
• This release contains 3,588 datasets (114,907 assays), in particular:
  • 837 RNA-seq and 21 proteomics datasets, of which 179 report baseline gene expression, across a total of 43 different organisms;
  • 805 datasets reporting expression in plants;
  • 3,409 datasets studying samples in 9,934 differential comparisons across 47 different organisms.
  • 62 overall species count

New experiments

• RNA-Seq of zebrafish embryos with wdr37 missense variant compared to wild type
• RNA-Seq of the liver of hypercholesterolemic mice treated by either ticagrelor, clopidogrel, or control
• Transcriptome analysis of human brain microvascular endothelial cells response to interactive DIII domain of protein E of WNV and interactive DIII domain of protein E of TBEV using RNA-seq
• RNA-Seq of rat myocardial slices cultured with biomimetic electromechanical stimulation
• RNA-Seq of chicken breast samples treated with chronic heat stress
• RNA-seq of neuronal SOX2-ablated murine suprachiasmatic nuclei against wild-type littermate controls

• RNA-seq in GR18 cell line to identify genes regulated by the Glucocorticoid Receptor (24h treatment)

• New Baseline experiments
  • RNA-sequencing of 465 lymphoblastoid cell lines from the 1000 Genomes
  • RNA-seq analysis of six cell line models for haematopoiesis: Project 1 of Open Targets - Epigenomes of Cell Lines
  • Human RNA-seq time-series of the development of seven major organs
  • Rat RNA-seq time-series of the development of seven major organs

Expression Atlas release 31 – May 2019

Data statistics

• Ensembl 96 / Ensembl Genomes 43 / WormBase ParaSite 12 gene annotations and array design probe set mappings.
• This release contains 3,564 datasets (112,229 assays), in particular:
  • 809 RNA-seq and 21 proteomics datasets, of which 173 report baseline gene expression, across a total of 42 different organisms;
  • 804 datasets reporting expression in plants;
  • 3,391 datasets studying samples in 9,852 differential comparisons across 47 different organisms.
  • 61 overall species count.

New experiments

• Expression Signatures in Polyarticular JIA Show Heterogeneity and Offer a Molecular Classification of Disease Subsets
• RNA seq of fluid shear stress treated mouse Pkd1-/- renal epithelial cells
• RNA-seq of Arabidopsis thaliana wild-type and a putative chloroplast ribosome biogenesis mutant AtRsgA homozygous knockout
• Genetics of gene expression across innate immune stimulation in primary monocytes
• Whole Blood Transcriptome Profiling in Juvenile Idiopathic Arthritis and Inflammatory Bowel Disease
• Comprehensive Analysis of Gene Expression Patterns in Friedreich’s Ataxia Fibroblasts by RNA Sequencing Reveals Altered Levels of Protein Synthesis Factors and Solute Carriers

• A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Microarray Analysis of Human Blood and Intestinal Biopsy Samples from a Phase 2b, Double-blind, Placebo-controlled Study of Ustekinumab in Crohn’s Disease

• New Baseline experiments
  • A comprehensive reference transcriptome for Brachypodium distachyon grain development incorporating key developmental transitions and identifying potential regulators
  • Chicken RNA-seq time-series of the development of seven major organs
  • A transcriptional map following the developmental trajectory of the Arabidopsis stomatal lineage

Expression Atlas release 30 – March 2019

Data statistics

• Ensembl 95 / Ensembl Genomes 42 / WormBase ParaSite 12 gene annotations and array design probe set mappings.
• This release contains 3,514 datasets (105,523 assays), in particular:
  • 782 RNA-seq and 21 proteomics datasets, of which 165 report baseline gene expression, across a total of 42 different organisms;
  • 796 datasets reporting expression in plants;
  • 3,349 datasets studying samples in 9,631 differential comparisons across 45 different organisms.
  • 60 overall species count.

New experiments

• RNA-sequencing of the mRNA transcriptome in blood, across three time-points in severe psoriasis patients treated with the tumor necrosis factor (TNF) inhibitor, etanercept
• Regional CNS immune fingerprint in chronic peripheral inflammation
• Transcriptional analysis of primary human monocyte-derived dendritic cells (moDCs) infected with different Zika virus strains and YF17D virus
• RNA-Seq of developing shoot apical meristems of barley cultivar Golden Promise (null segregant and Ubi::HvFT3 overexpressor) grown under long- and short-day photoperiods
• RNASeq data analysis of wild type and reverb alpha knockout cells from mouse liver, at different time points, with or without DEX treatment

• Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish

• New Baseline experiments
  • RNA-seq of in vitro differentiation of human embryonic stem cells into cortical neurons over 77 days
  • Transcription profiling by high throughput sequencing of of egg cells, sperm cells and vegetative cells from Oryza sativa ssp. japonica

Expression Atlas release 29 – November 2018

Data statistics

• Ensembl 94 / Ensembl Genomes 41 / WormBase ParaSite 11 gene annotations and array design probe set mappings.
• This release contains 3,451 datasets (104,099 assays), in particular:
  • 736 RNA-seq and 21 proteomics datasets, of which 164 report baseline gene expression, across a total of 42 different organisms;
  • 794 datasets reporting expression in plants;
  • 3,287 datasets studying samples in 9,378 differential comparisons across 44 different organisms.

New experiments

• Compatible and incompatible infection of potato by nematode Globodera rostochiensis
• mRNAseq of Drosophila S2 cells after knockdown of EJC components developmental stages
• RNA-seq of 23 tissues spanning vegetative and reproductive stages of maize development
• RNA-seq of Chlamydomonas reinhardtii under diel conditions to identify cycling genes
• Transcription profiling by high throughput sequencing of 10 accessions of Aegilops tauschii

• RNA-seq of total and polysomal RNA of clk-1(qm30) mutants in Caenorhabditis elegans

• New proteomics experiments
  • Colorectal cancer cell line proteomes
  • Deep proteome of HeLa, A549, HCT116, MCF7, and SHSY5Y cell lines
  • Comparative proteomic analysis of eleven common cell lines
  • The Proteome of Primary Prostate Cancer
    and Corresponding Nonmalignant Tissue
  • Panel of 20 human breast cell lines and four clinical tumors
  • Proteomics characterization of human colon and rectal cancer
  • Pharmacoproteomic characterisation of human colon and rectal cancer
  • Global Proteome Analysis of the NCI-60 Cell Line Panel
  • Deep proteomic profiling of luminal breast cancer progression
  • Systems-wide quantitative proteomic study of breast cancer tumours
  • Integrative proteomic profiling of ovarian cancer cell lines

Expression Atlas release 28 – August 2018

Data statistics

• Ensembl 92 / Ensembl Genomes 39 / WormBase ParaSite 10 gene annotations and array design probe set mappings.
• This release contains 3,388 datasets (101,247 assays), in particular:
  • 691 RNA-seq and 10 proteomics datasets, of which 150 report baseline gene expression, across a total of 40 different organisms;
  • 791 datasets reporting expression inplants;
  • 3,238 datasets studying samples in 9,254 differential comparisons across 45 different organisms.

Expression Atlas release 27 – April 2018

Data statistics

• Ensembl 91 / Ensembl Genomes 38 / WormBase ParaSite 9 gene annotations and array design probe set mappings.
• This release contains 3,328 datasets (119,472 assays), in particular:
  • 653 RNA-seq and 12 proteomics datasets, of which 154 report baseline gene expression, across a total of 42 different organisms;
  • 780 datasets reporting expression in plants;
  • 3,177 datasets studying samples in 9,007 differential comparisons across 46 different organisms.

New experiments

• New plant species
  • RNA-seq of a E-type and a Z-type cultivar of sugar beet at five different developmental stages (Beetroot)
  • RNA-seq of Brassica napus seeds at different developmental stages (Rapeseed)
  • RNA-seq of Brassica napus in response to PA23 in the presence or absence of Sclerotinia sclerotiorum (Rapeseed)
  • RNA-seq of Chlamydomonas reinhardtii under diel conditions to identify cycling genes (Green algae)
  • RNA-seq of Chlamydomonas reinhardtii response to nitrogen deprivation in cht7 mutant plants (Green algae)
  • RNA-seq of banana in vitro roots under mild osmotic stress (Banana)
  • RNA-seq of banana fruit development (Banana)
  • RNA-seq of Prunus persica roots and leaves under drought stress (Peach)
  • Transcriptome sequencing of Foxtail millet Setaria italica for different tissues (Foxtail millet)
  • RNA-seq of two Trifolium pratense genotypes, Tripo and Lasang, from early to late developmental stages of flower development (Red clover)
• New proteomics experiments
  • Deep Proteomics of Mouse Skeletal Muscle
  • Cell-Type-Resolved Quantitative Proteomics of Murine Liver
  • Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse
  • A tissue-specific atlas of mouse protein phosphorylation and expression
  • Murine protein tissue atlas of heavily vascularized organs and cells adjacent to the blood plasma
  • Atxn2-Knock-Out mice show branched chain amino acids and fatty acids pathway alterations
  • mESC shotgun and positional proteomics based on deep proteome sequence database (derived from RIBOseq data)
  • Fractionation-dependent improvements in proteome resolution in the mouse hippocampus by IEF LC-MS/MS

New features

• Single gene results in an experiment page now include a new transcript expression visualisation. Please read the help section on Transcript quantification to know more.

Expression Atlas release 26 – October 2017

Data statistics

• Ensembl 90 / Ensembl Genomes 37 / WormBase ParaSite 9 gene annotations and array design probe set mappings.
• This release contains 3,166 datasets (118,209 assays), in particular:
  • 565 RNA-seq and 4 proteomics datasets, of which 134 report baseline gene expression, across a total of 32 different organisms;
  • 734 datasets reporting expression in plants;
  • 3,035 datasets studying samples in 8,488 differential comparisons across 32 different organisms.

New experiments

• New cancer data set from the Sanger Institute Genomics of Drug Sensitivity in Cancer (GDSC):
  • Sanger Genomics of Drug Sensitivity in Cancer Project (GDSC) RNA-seq cancer cell line gene expression data
• New non–small-cell lung cancer data:
  • RNA-seq of 199 non-small cell lung carcinoma patients and 19 paired normal lung tissues
  • RNA-seq of primary tumors from 79 small cell lung cancer patients and 7 normal lung tissue

New features

• Improved search with special characters. You can now search for conditions like 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide.

Expression Atlas release 25 – August 2017

Data statistics

• Ensembl 89 / Ensembl Genomes 36 / WormBase ParaSite 9 gene annotations and array design probe set mappings.
• This release contains 3,126 datasets (113,148 assays), in particular:
  • 537 RNA-seq and 4 proteomics datasets, of which 131 report baseline gene expression, across a total of 32 different organisms;
  • 731 datasets reporting expression in plants;
  • 2,998 datasets studying samples in 8,391 differential comparisons across 33 different organisms.

New experiments

• First pig baseline RNA-seq data (Sus scrofa):
  • RNA-seq of different tissues from Sus scrofa

New features

• All RNA-Seq baseline experiments are displayed using TPMs by default where available. There is a new radio button to switch to FPKMs if desired.
  • Example: Open Targets RNA-seq analysis of six cell lines in TPM cf. the same experiment in FPKM.
• You can download results from the Gene Set Enrichment results page by clicking on the Download results button on the top right.
• Now you can choose what data to download in the experiment page: the highest expressed genes as displayed in the heatmap, or all results matching your query.
  • Example: click on the down-pointing arrow in the Download button, located to the right above the heatmap, to download e.g. all genes with expression level above 10 TPM in Illumina Body Map, Download all data or only the top 50 genes sorted by expression level, Download table content.

Expression Atlas release 24 – May 2017

Data statistics

• Ensembl 88 / Ensembl Genomes 35 / WormBase ParaSite 9 gene annotations and array design probe set mappings.
• This release contains 3,116 datasets (104,386 assays), in particular:
  • 529 RNA-seq and 3 proteomics datasets, of which 127 report baseline gene expression, across a total of 31 different organisms;
  • 729 datasets reporting expression in plants;
  • 2,992 datasets studying samples in 8,368 differential comparisons across 33 different organisms.

New experiments

• New baseline RNA-seq data from the Human Induced Pluripotent Stem Cells Initiative (HipSci):
  • RNA-seq of coding RNA in human fibroblasts, Peripheral Blood Mononuclear Cells (PBMCs) and induced pluripotent stem cells (iPS cells)
• Updated version of Genotype-Tissue Expression (GTEx) Project with 18,736 assays:
  • RNA-seq from 52 human tissue samples from the Genotype-Tissue Expression (GTEx) Project

New Home Page

• We have updated our home page with more useful links to species-specific experiments or other large scale projects.

On-the-fly gene set overlap analysis

• Our GeneSet Enrichment API now has a front page. Click on “Gene Set Enrichment” next to “Search” on our home page and input a set of gene identifiers.
  • Example result: Arabidopsis thaliana

New Experiment Page

• Our experiment pages have been re-organised and updated with a new style of heatmap. See help pages for more details while exploring an example:
  • RNA-seq from 52 human tissue samples from the Genotype-Tissue Expression (GTEx) Project

Expression Atlas release 23 – February 2017

Data statistics

• Ensembl 87 / Ensembl Genomes 34 gene annotations and array design probe set mappings.
• This release contains 3,063 datasets (125,327 assays), in particular:
  • 494 RNA-seq and 3 proteomics datasets, of which 122 report baseline gene expression, across a total of 30 different organisms;
  • 703 datasets reporting expression in plants;
  • 2,941 datasets studying samples in 8,246 differential comparisons across 33 different organisms.

New experiments

• New mouse embryo data from the Mouse Genetics Project/DMDD project:
  • Strand-specific RNA-seq of somite-staged whole embryos comparing 11 homozygous mutants against wild type
• New human baseline expression on prenatal brain tissues from the Human Developmental Biology Resource HDBR:
  • RNA-seq from 23 time points and 21 different embryonic brain tissues

New Features

• Data on cross-experiment, organism part heatmaps can now be filtered by anatomical systems and gene expression. Explore example:
  • REG1B (human)

Expression Atlas release 22 – December 2016

Data statistics

• Ensembl 86 / Ensembl Genomes 33 gene annotations and array design probe set mappings.
• This release contains 3,025 datasets (123,194 assays), in particular:
  • 485 RNA-seq and 3 proteomics datasets, of which 121 report baseline gene expression, across a total of 30 different organisms;
  • 698 datasets reporting expression in plants;
  • 2,904 datasets studying samples in 8,117 differential comparisons across 31 different organisms.

New experiments

• New proteomics data from the Human Induced Pluripotent Stem Cells Initiative (HipSci):
  • Baseline protein expression for 18 IPS cell lines
• Updated version of Genotype-Tissue Expression (GTEx) Project with 9,347 assays:
  • RNA-seq from 52 human tissue samples from the Genotype-Tissue Expression (GTEx) Project
• First experiment on green monkey (Chlorocebus aethiopssabaeus):
  • RNA-seq of six tissues at different ages
• New plant species:
  • Transcription profiling of seven tissues of Brassica oleracea (wild cabbage)
  • Transcription profiling of 15 tissues of Solanum tuberosum (potato)

Expression Atlas release 21 – September 2016

Data statistics

• Ensembl 85 / Ensembl Genomes 32 gene annotations and array design probe set mappings.
• This release contains 2,968 datasets (110,249 assays), in particular:
  • 444 RNA-seq and 2 proteomics datasets, of which 108 report baseline gene expression, across a total of 25 different organisms;
  • 632 datasets reporting expression in plants;
  • 2,860 datasets studying samples in 8,015 differential comparisons across 30 different organisms.

New Features

• Data on heatmaps can now be sorted by gene and protein expression rank. Explore example:
  • REG1B (human)
• Faceted search is now available for keyword-based gene or sample property queries. Explore example queries:
  • liver (any organism)
  • HSP18.1 gene and leaf (any organism)

New experiments

• Mouse embryo data from the DMDD project:
  • Strand-specific RNA-seq of somite-staged second generation genotypically wild-type embryos of mixed G0 lineage from the Mouse Genetics Project/DMDD
  • Strand-specific RNA-seq of somite-staged pure-bred wild-type mouse embryos from the Mouse Genetics Project/ DMDD
• Zebrafish embryo data from the Vertebrate Genetics and Genomics Group at the Wellcome Trust Sanger Institute:
  • Baseline expression from transcriptional profiling of zebrafish developmental stages

Expression Atlas release 20 – June 2016

Data statistics

• Ensembl 84 / Ensembl Genomes 31 gene annotations and array design probe set mappings.
• This release contains 2,914 datasets (106,062 assays), in particular:
  • 401 RNA-seq and 2 proteomics datasets, of which 96 report baseline gene expression, across a total of 23 different organisms;
  • 671 datasets reporting expression in plants;
  • 2,818 datasets studying samples in 7,863 differential comparisons across 30 different organisms.

New heatmap

• This release launches the new style of heatmap on the gene/gene-set page. The changes include:
  • resizable, zoom-able display
  • assigning expression levels to low, medium, high
• Examples:
  • Foxo3 (mouse)
  • Respiratory gaseous exchange

New feature: similar expression patterns

• This release includes a new feature for exploring genes with similar expression patterns across conditions in baseline experiments. Explore examples:
  • In Vitis vinifera development
  • In Oryza sativa tissues
• For more information please see FAQ: How are similarly expressed genes computed?

New experiments

• This release of Expression Atlas includes datasets on tomato (Solanum lycopersicum), a new species for us! We now have four baseline experiments, studying fruit development and profiling various tissues:
  • Transcription profiling by high throughput sequencing of the five principal tissues of the pericarp from tomato fruits at their maximal growth phase
  • Transcription profiling by high throughput sequencing of tomato root, leaf, flower (2 stages) and fruit (6 stages)
  • Transcription profiling by high throughput sequencing along three longitudinal sections of six stages during tomato fruit development
  • Transcription profiling by high throughput sequencing of tomato fruit at four developmental stages
• As well as the above baseline datasets, we can also showcase seven differential expression studies on tomato:
  • Transcription profiling by high throughput sequencing of tomato Rio Grande prf3 leaves challenged with either the flgII-28 peptide or different bacterial strains
  • Transcription profiling by high throughput sequencing of two tomato nearly isogenic lines that differ for the allele at fw3.2 in Yellow Stuffer background
  • Transcription profiling by high throughput sequencing of flower buds from two tomato nearly isogenic lines that differ for the allele at fw3.2 in Yellow Stuffer background
  • Transcription profiling by high throughput sequencing of leaves of resistant (RG-PtoR) and susceptible (RG-prf3 and RG-prf19) tomato plants treated with Pseudomonas syringae pv. tomato str. DC3000
  • Transcription profiling by high throughput sequencing of leaves of resistant (RG-PtoR) tomato plants treated with different Pst DC3000 mutant strains
  • Transcription profiling by high throughput sequencing of immature green and red ripe tomato fruits from plants over-expressing SIGLK1 and SIGLK2
  • Transcription profiling by high throughput sequencing of tomato SUN and wild type fruit tissues
• The latest release also sees our first experiment studying baseline expression in different Arabidopsis tissues, a new dataset on tonsil from the BLUEPRINT Epigenome project as well as updates to the previously-added BLUEPRINT dataset on haematopoiesis, and RNA-seq data from Open Targets showing baseline expression of lung disease cell line models.

Bioconductor package out now

• The Expression Atlas R package is now available as of version 3.3 of Bioconductor. Using this package you can search for Atlas datasets and download the data from inside an R session or script. Please see the package vignette for more information.

Expression Atlas release 19 – April 2016

Data statistics

• Ensembl 84 / Ensembl Genomes 31 gene annotations and array design probe set mappings.
• This release contains 2,738 datasets (100,801 assays), in particular:
  • 261 RNA-seq and 2 proteomics datasets, of which 72 report baseline gene expression, across a total of 22 different organisms;
  • 621 datasets reporting expression in plants;
  • 2,666 datasets studying samples in 7,496 differential comparisons across 29 different organisms.

Expression Atlas release 18 – April 2016

Data statistics

• Ensembl 84 / Ensembl Genomes 30 gene annotations and array design probe set mappings.
• This release contains 2,688 datasets (99,162 assays), in particular:
  • 224 RNA-seq and 2 proteomics datasets, of which 60 report baseline gene expression, across a total of 21 different organisms;
  • 602 datasets reporting expression in plants;
  • 2,626 datasets studying samples in 7,411 differential comparisons across 28 different org

Expression Atlas release 17 – January 2016

Data statistics

• Ensembl 83 / Ensembl Genomes 30 gene annotations and array design probe set mappings.
• This release contains 2,620 datasets (97,484 assays), in particular:
  • 167 RNA-seq and 1 proteomics dataset, of which 47 report baseline gene expression, across a total of 19 different organisms;
  • 582 datasets reporting expression in plants;
  • 2,573 datasets studying samples in 7,281 differential comparisons across 29 different organisms.
• R experiment summary objects for RNA-seq datasets now use the new RangedSummarizedExperiment class from the Summarized Experiment Bioconductor package. See the help page for more details about how to use them.

Expression Atlas release 16 – December 2015

Data statistics

• Ensembl 83 / Ensembl Genomes 29 gene annotations and array design probe set mappings.
• This release contains 2,574 datasets (98,278 assays), in particular:
  • 157 RNA-seq and 1 proteomics dataset, of which 46 report baseline gene expression, across a total of 19 different organisms;
  • 568 datasets reporting expression in plants;
  • 2,527 datasets studying samples in 7,119 differential comparisons across 26 different organisms.
• This release launches the new gene and gene-set interface, available for species-specific gene queries or gene-set identifier queries, via Gene Ontology (GO) or Reactome IDs, e.g.
  • Foxo3 (mouse)
  • Respiratory gaseous exchange
• The new pages feature faceted search in Differential expression and Baseline Expression tabs, including
  • Filtering differential expression by Species, Experiment, Variables, up or down regulation etc.
  • Ability to show/hide baseline experiments studying other conditions than just tissues, e.g. cell lines, cell types, etc.
  • Anatomograms can now be shown/hidden as required.

Baseline experiment types, except for cell lines, can be viewed on a heatmap.

Expression Atlas release 15 – October 2015

Data statistics

• Ensembl 82 / Ensembl Genomes 29 gene annotations and array design probe set mappings.
• This release contains 2,373 datasets (93,057 assays)
• In particular, this release contains:
  • 119 RNA-seq and 1 proteomics dataset, of which 43 report baseline gene expression, across a total of 17 different organisms;
  • 424 datasets reporting expression in plants;
  • 2,330 datasets studying samples in 6,345 differential comparisons across 25 different organisms.

Expression Atlas release 14 – October 2015

Data statistics

• Ensembl 82 / Ensembl Genomes 28 gene annotations and array design probe set mappings.
• This release contains 2,162 datasets (86,980 assays), including:
  • 19 Fetal Tissues from NIH Roadmap Epigenomics Mapping Consortium (64 assays)
• In particular, this release contains:
  • 119 RNA-seq and 1 proteomics dataset, of which 43 report baseline gene expression, across a total of 17 different organisms;
  • 410 datasets reporting expression in plants;
  • 2,119 datasets studying samples in 5,752differential comparisons across 25 different organisms.

Expression Atlas release 13 – September 2015

Data statistics

• Ensembl 81 / Ensembl Genomes 28 gene annotations and array design probe set mappings.
• This release contains 1,895 datasets (81,255 assays), including:
  • Re-analysis of Pandey lab’s draft of the human proteome (30 assays) - our first protemics dataset!
  • RNA-seq of coding RNA from sheep embryonic, juvenile and adult tissues (235 assays)
  • RNA-seq of various Sorghum bicolor (BTx623) tissues: flowers, vegetative and floral meristems, embryos, roots and shoots (17 assays)
• In particular, this release contains:
  • 117 RNA-seq datasets, of which 42 of these report [baseline] (https://www.ebi.ac.uk/gxa/baseline/experiments) gene expression, across a total of 15 different organisms;
  • 397 datasets reporting expression in plants;
  • 1,853 datasets studying samples in 4,925 differential comparisons across 25 different organisms.

Expression Atlas release 12 – August 2015

Data statistics

• Ensembl 81 / Ensembl Genomes 28 gene annotations and array design probe set mappings.
• This release contains 1,572 datasets (69,239 assays), including:
  • RNA-seq of 934 human cancer cell lines from the Cancer Cell Line Encyclopedia (30,088 assays)
• In particular, this release contains:
  • 96 RNA-seq, of which 38 of these report baseline gene expression, across a total of 15 different organisms;
  • 389 reporting expression in plants;
  • 1,534 studying samples in 4,287 differential comparisons across 25 different organisms.
  • A much broader coverage of tissues in mouse anatomograms, c.f. mouse SFTPA gene expression

Expression Atlas release 11 – July 2015

Data statistics

• Ensembl 80 / Ensembl Genomes 27 gene annotations and array design probe set mappings.
• This release contains 1,107 datasets (24,048 assays), including:
  • RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice tissues in RIKEN FANTOM5 project
• In particular, this release contains:
  • 68 RNA-seq, of which 30 of these report baseline gene expression, across a total of 16 different organisms;
  • 385 reporting expression in plants;
  • 1,082 studying samples in 2,923 differential comparisons across 24 different organisms.
  • A much broader coverage of tissues in human anatomograms, c.f. human SFTPA2 gene expression

Expression Atlas release 10 – June 2015

Data statistics

• Ensembl 80 / Ensembl Genomes 26 gene annotations and array design probe set mappings.
• We are proud to announce that release contains 1,051 datasets (yes, we did celebrate!), now including:
  • RNA-seq from 53 human tissue samples from the Genotype-Tissue Expression (GTEx) Project
  • RNA-seq of 675 commonly used human cancer cell lines (Genentech)
  • RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice cells in RIKEN FANTOM5 project
• In particular, this release contains:
  • 67 RNA-seq, of which 29 of these report baseline gene expression, across a total of 16 different organisms;
  • 366 reporting expression in plants;
  • 1,022 studying samples in 2,704 differential comparisons across 24 different organisms.

Expression Atlas release 9 – March 2015

Data statistics

• Ensembl 79 / Ensembl Genomes 26 gene annotations and array design probe set mappings.
• This release contains 935 datasets, including:
  • 56 RNA-seq, of which 26 of these report baseline gene expression, across a total of 16 different organisms;
  • 261 reporting expression in plants;
  • 909 studying samples in 2,306 differential comparisons across 20 different organisms.

Expression Atlas release 8 – March 2015

Data statistics

• Ensembl 79 / Ensembl Genomes 25 gene annotations and array design probe set mappings.
• This release contains 932 datasets, including:
  • 56 RNA-seq, of which 26 of these report baseline gene expression, across a total of 16 different organisms;
  • 258 reporting expression in plants;
  • 906 studying samples in 2,291 differential comparisons across 20 different organisms.
• New data sets of note:
  • RNA-seq of 39 human cancer cell lines that are in the NCI-60 set from the Cancer Cell Line Encyclopedia
  • RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of human tissues in RIKEN FANTOM5 project
• Differential expression for RNA-seq data is now calculated using DESeq2 method.
• Users searching for a single gene within a baseline experiment are now able to see how expression varies across biological replicates for each condition - by selecting Display variation option. This is currently a prototype - we welcome any feedback you may have. Please use the feedback button on the top right hand side of all Atlas pages.

Expression Atlas release 7 – January 2015

Data statistics

• Ensembl 78 / Ensembl Genomes 25 gene annotations and array design probe set mappings.

• This release contains 909 datasets, including 57 RNA-seq experiments. 24 of these report baseline gene expression, across a total of 16 different organisms. 885 datasets study samples in 2,226 differential comparisons across 20 different organisms.

• RNA-seq of coding RNA from tissue samples of 122 human individuals representing 32 different tissues data set is now available;

Expression Atlas release 6 – December 2014

Data statistics

• Ensembl 78 / Ensembl Genomes 24 gene annotations and array design probe set mappings.

• This release contains 873 datasets, including 50 RNA-seq experiments. 23 ofthese report baseline gene expression, across a total of 16 different organisms. 850 datasets study samples in 2,121 differential comparisons across 20 different organisms.

• Please note that splice variant expression quantification is no longer available in Atlas. We have also replaced Cufflinks2 with HTSeq for gene expression quantification.

• By clicking on the link highlighted on the image below, the experiment data can now by filtered by gene/protein keywords that were mined from the supporting publication by Europe PubMed Central. Click here to try it out.

Expression Atlas release 5 – November 2014

Data statistics

• Ensembl 77 / Ensembl Genomes 24 gene annotations and array design probe set mappings.
• This release contains 844 datasets, including 50 RNA-seq experiments. 22 of these report baseline gene expression, across a total of 16 different organisms. 822 datasets study samples in 2,032 differential comparisons across 20 different organisms.
• Plant experiments, for example our first RNA-seq maize data set, now allow users to display expression in the Genome Browser.

Expression Atlas release 4 – October 2014

Data statistics

• Ensembl 77 gene annotations and array design probe set mappings.
• This release contains 802 datasets, including 47 RNA-seq experiments. 21 of these report baseline gene expression, across a total of 15 different organisms. 781 datasets study samples in 1,937differential comparisons across 20 different organisms.
• Gene pages now show a combined comparative view for gene expression across multiple baseline datasets.

• Hierarchical clustering of the top 100 most variably expressed genes is now performed for each baseline dataset.

• Three new anatomograms are now available, for Anolis carolinensis, Xenopus tropicalis and Tetraodon nigroviridis.

Expression Atlas release 3 – August 2014

Data statistics

• Ensembl 76 / Ensembl Genomes 23 gene annotations and array design probe set mappings;
• 709 experiments, including 39 RNA-seq experiments (13baseline, 26 differential), studying samples in 1,684 differential comparisons and 24 organisms (see below for breakdown of comparisons per organism);
• All Human RNA-seq experiments have been re-analysed against the new assembly (GRCh38), e.g. RNA-seq of coding RNA from tissue samples of 95 human individuals representing 27 different tissues;
• Baseline expression levels available for genes and transcripts in 75 tissues, 21 cell lines, 7 cellular components, 39 developmental stages and 3 RNA types;
• Quality control reports, e.g. FASTQ QC and Mapping, are now available for all RNA-seq experiments;
• EFO-based autocomplete for experimental conditions is now available on the main Atlas search page. Please see ‘How to search’ section of Atlas help page for more details. The main search interface also now allows users to restrict search to a single organism;
• User queries in the main Atlas search interface are expanded using the latest EFO. This means that if you search for e.g. “cancer”, you will also see results with terms such as “carcinoma”, “malignant tumour”, and other synonyms and children of the cancer entry in EFO;
• Gene set overlap analysis is performed using the Piano package from Bioconductor. In each differential experiment, for each comparison, enrichment of terms from GO, InterPro, and Reactome is tested for within the set of differentially expressed genes, using Fisher’s exact test. Plots showing maximum top ten GO, Interpro and Reactome terms enriched within the differentially expressed genes for each comparison are now available for each differential experiment in Atlas. Please see Differential Atlas help for more information.
• For differential expression experiments you can now download a file containing the expression data and meta-data that you can load into R. Please see Expression Atlas data in R help for more information;
• Differential and Baseline Expression can now be visualised on Ensembl and Ensembl Genomes Genome Browser. Please see “Can I view the results in the Ensembl browser?” in our FAQ for more information.

Expression Atlas release 2 – April 2014

Data statistics

• Ensembl 75 / Ensembl Genomes 22 gene annotations and array design probe set mappings;
• 401 experiments, including 24 RNA-seq experiments (8 baseline, 16 differential), studying samples in 19 species and 653 differential comparisons (see below for breakdown of comparisons per experimental variable type);
• Average number of citations per experiment: 42 (courtesy of Europe PubMed Central);
• Baseline expression levels available for genes and transcripts in 54 tissues, 21 cell lines, 5 cellular components, 5 developmental stages and 3 RNA types;
• RNA-seq of coding RNA from tissue samples of 95 human individuals representing 27 different tissues data set is now available;
• Automatic quality control (QC) for Microarray experiments in operation; QC reports available to users, e.g. Transcription profiling by array of human PMA-activated MM6 cells with cyclin T1 knockdown

Expression Atlas release 1 – December 2013

Welcome to the new Expression Atlas service! The old Expression Atlas and its underlying data will no longer be updated or maintained, but limited support will be offered while the process of re-curation, re-analysis and transferring of experiments to the new Expression Atlas is on-going.

We would like to thank our users for their continuous support, and encourage them to help us shape the new Expression Atlas by:

• providing us with feedback via the EBI Support & feedback form;
• contacting us if any experiments of interest are included in the old Expression Atlas, but have not made their way into the new Expression Atlas yet. We will then prioritise their transfer.

Enjoy the new Expression Atlas!