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!