Single Cell Expression Atlas release 21 – September 2024

Data statistics

• Ensembl 104 / Ensembl Genomes 51 / WormBase ParaSite 15 gene annotations.
• This release contains 381 single cell RNA-Seq studies, consisting of 24,323,556 cells, of which 13,519,191 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 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)