Browse baseline experiments
These datasets show baseline gene expression for many different tissues and cell types from a wide range of species, from human and mouse to Arabidopsis and maize. In Expression Atlas, "baseline" expression is the expression level of each gene in normal, untreated conditions. All baseline experiments are either RNA-seq or proteomics data. Each experiment is manually curated to a high standard, and RNA expression levels are calculated using the iRAP pipeline.
Homo sapiens
- Age - Matson et al., 2019 (69 assays)
- Alasoo et al 2017 - Cell lines (673 assays)
- BLUEPRINT EpiVar Project - Cell Types (614 assays)
- Cell Lines - 675 Genentech (622 assays)
- Cell Lines - 7 Melanoma (7 assays)
- Cell Lines - CCLE (1019 assays)
- Cell Lines - Cancer Genome Project (462 assays)
- Cell Lines - ENCODE (166 assays)
- Cell Lines - Geuvadis consortium (462 assays)
- Cell Lines - OpenTargets - Haematopoiesis (18 assays)
- Cell Lines - OpenTargets - Lung (7 assays)
- Cell Lines - Project 6 of Open Targets - Epigenomes of Cell Lines (12 assays)
- Cell Types - BLUEPRINT common haemopoetic cells (66 assays)
- Cell Types - BLUEPRINT rare hematopoietic cells (96 assays)
- Cell Types - BLUEPRINT tonsil plasma cells (4 assays)
- Cell Types - Fetal endothelial cells - Holloway et al (128 assays)
- Cell Types - Splenic B cells - Chappert et al (12 assays)
- Cell lines - 196 HipSci (397 assays)
- Cell lines - Breast carcinoma - Jastrzebski et al (30 assays)
- Cell lines - HipSci - 106 sensory neuronal cell lines (434 assays)
- Cells - Lymph and blood endothelial cells (6 assays)
- Cortical differentiation - CORTECON (44 assays)
- Developmental Stages - Kraiczy et al intestinal cells (30 assays)
- EDTL Diamonds project - Disease (411 assays)
- GTEX - organism part (17350 assays)
- Hallstrom et al., 2014 - Organism part (171 assays)
- Klpinen et al., 2017 HipSci - Cell Lines (389 assays)
- Lee et al., 2016 - Individual (24 assays)
- Neuroblastoma cell lines - Duffy et al (8 assays)
- Sexes - Skeletal muscle (26 assays)
- Sexes - Skeletal muscle (80 assays)
- Tissues - 19 NIH Epigenomics Roadmap (64 assays)
- Tissues - 3 Glioma subtypes (49 assays)
- Tissues - 32 Uhlen's Lab (179 assays)
- Tissues - 68 FANTOM5 project (96 assays)
- Tissues - ENCODE (M. Snyder lab) (25 assays)
- Tissues - HDBR developing brain (613 assays)
- Tissues - Illumina Body Map (16 assays)
- Tissues - Mammalian Kaessmann (12 assays)
- Tissues - Pan-Cancer Analysis of Whole Genomes (3372 assays)
- Tissues - Pan-Cancer Analysis of Whole Genomes (by individual) (1359 assays)
- Tissues, developmental stages - Human - Moreira et al (287 assays)
- Villa et al., 2020 - Cell Type (24 assays)
- Zhu et al., 2018 - Organism part (14 assays)
- iPSCs - GENESiPS (317 assays)
- van de Bunt et al 2015 - Individual (118 assays)
- Bing et al., 2019 - Tissue - liver fractions (41 assays)
- Cell lines - colorectal cancer (50 assays)
- ColCancer2023_Cell lines - colon cancer cell lines - Robles et al. 2022 (3 assays)
- ColCancer2023_Cell lines - disease - Novikova et al. 2020 (30 assays)
- ColCancer2023_Disease - colon adenoma - Sohier et al. 2020 (62 assays)
- ColCancer2023_Disease - colon and rectal carcinoma - Zhang et al. 2014 (90 assays)
- ColCancer2023_Disease - colorectal cancer - Costanza et al. 2018 (12 assays)
- ColCancer2023_Disease - colorectal cancer - Costanza et al. 2018 /2 (15 assays)
- ColCancer2023_Disease - colorectal cancer - Ikeda et al. 2021 (68 assays)
- ColCancer2023_Disease - colorectal cancer - MarÃn-Vicente et al. 2019 (5 assays)
- ColCancer2023_Disease - colorectal cancer - Sethi et al. 2015 (16 assays)
- ColCancer2023_Disease - colorectal cancer - Slebos et al. 2015 (74 assays)
- ColCancer2023_Disease - colorectal cancer - WiÅniewski et al. 2015 (32 assays)
- ColCancer2023_Disease - response to treatment - Strybel et al. 2022 (79 assays)
- Doll et al., 2017 - Organism part (42 assays)
- Guette et al., 2019 - Disease - breast cancers (144 assays)
- Guo T. et al., 2016 - Cell lines - NCI-60 cancer cell lines (120 assays)
- Guo et al., 2018 - Disease - hepatocellular carcinoma (76 assays)
- Guo et al., 2018 - Disease - prostate cancers and hyperplasia (60 assays)
- Guo et al., 2018 - disease (210 assays)
- Human2021_Tissues - Wang et al. 2019 (31 assays)
- Johnson ECB et.al., 2020 - Disease (84 assays)
- Johnson et al., 2020 - BSLA - Disease (46 assays)
- Johnson et al., 2020 - Baltimore Longitudinal Study of Aging - Disease (44 assays)
- Johnson et al., 2020 - Banner Sun Health Research Institute collection -Disease (178 assays)
- Johnson et al., 2020 - Disease (65 assays)
- Johnson et al., 2020 - Mayo Clinic Brain Bank - Disease (198 assays)
- Johnson et al., 2020 - University of Pennsylvania School of Medicine Brain Bank - Disease (354 assays)
- Li et al., 2020 Parkinson's disease tissues (12 assays)
- Linscheid et al., 2020 â Tissues - heart (21 assays)
- Liu Y et al., 2015 - Tissues - blood (234 assays)
- Mallis et al., 2020 - Tissues - umbilical artery (10 assays)
- McKetney J et.al., 2019 - Individual (26 assays)
- McKetney et al., 2019 â organism part - disease (40 assays)
- Mendonça CF, et.al., 2019 - Individual (103 assays)
- Proteomics - Cell Line - Colorectal cancer cell lines (44 assays)
- Proteomics - Cell Line - Comparative analysis of common cell lines (33 assays)
- Proteomics - Cell Line - Deep proteome of cancer cell lines (14 assays)
- Proteomics - Cell Line - Human colon and rectal cancer cell lines (65 assays)
- Proteomics - Cell Line - NCI-60 Panel (66 assays)
- Proteomics - Cell Line - Ovarian cancer cell lines (101 assays)
- Proteomics - Cell Lines - HipSci (18 assays)
- Proteomics - Cell line and Tissue - Breast cancer (88 assays)
- Proteomics - Tissue - Breast cancer - Pozniak et al. (103 assays)
- Proteomics - Tissue - Breast cancer - Tyanova et al. (40 assays)
- Proteomics - Tissue - Prostate cancer (36 assays)
- Proteomics - Tissues - Human Protein Atlas (83 assays)
- Proteomics - Tissues - Human Proteome Map (30 assays)
- Tissues - brain regions (77 assays)
- Tissues - breast - Gomig et al 2019 (12 assays)
- Tissues - breast - Groessl et al. 2014 (3 assays)
- Tissues - cerebellum and occipital lobe (15 assays)
- Tissues - colonic mucosa - Bennike et al. 2015 (10 assays)
- Tissues - colonic mucosa- Bennike et al. 2016 (8 assays)
- Tissues - corpus callosum and temporal lobe (4 assays)
- Tissues - ovary, pancreas, liver, subst. nigra (51 assays)
- Tissues - pineal gland (3 assays)
- Tissues - pituary gland (2 assays)
- Tissues - prefrontal cortex (4 assays)
- Tissues - temporal lobe (6 assays)
- Wang et al., 2018 - Mount Sinai Alzheimer'scohort - Disease (188 assays)
Aegilops tauschii
Anolis carolinensis
Arabidopsis lyrata
Arabidopsis thaliana
- Adrian et al 2015 (11 assays)
- Ages - 10 Klepikova et al (30 assays)
- Arabidopsis silique development - Chua et al (4 assays)
- Arabidopsis thaliana - ARAPORT11 (116 assays)
- Ecotypes - 17 Clark et al (51 assays)
- Ecotypes - 19 Gan et al (42 assays)
- Ecotypes - 9 Kurlovs et al. (54 assays)
- Huang et al 2017 - Root sampling site (9 assays)
- Mergner et al., 2020 - Organism part (56 assays)
- Narsai et al., 2017 - Time series (30 assays)
- Romanowski et al., 2020 - Timeseries (24 assays)
- Tissues - 4 Liu et al (4 assays)
- Tissues, genotypes - Pignatta et al., 2014 (30 assays)
- Wang et al., 2015 - Ecotype (24 assays)
- Wang et al., 2015 - Ecotype (64 assays)
- Wendrich et al., 2017 - Sampling site (24 assays)
- Yang et al., 2016 - Ecotype (12 assays)
- arabidopsis2023_Tissues - Mergner J et al. 2020 (30 assays)
Beta vulgaris subsp. vulgaris
Bos taurus
Brachypodium distachyon
Brassica napus
Brassica oleracea
Brassica rapa
Brassica rapa subsp. rapa
Caenorhabditis elegans
Chlamydomonas reinhardtii
Chlorocebus sabaeus
Drosophila melanogaster
Drosophila pseudoobscura
Equus caballus
Gallus gallus
Glycine max
- 4 Stages - Harada and Goldberg (273 assays)
- 8 Stages - Brown and Hudson (42 assays)
- Developmental Stages - 4 Goldberg et al (9 assays)
- Developmental Stages - 7 Goldberg et al (19 assays)
- Developmental Stages - 7 Jones and Vodkin (16 assays)
- Huang et al 2017 - Root sampling site (9 assays)
- Seed oil content - Goettel et al (9 assays)
- Seedling development - Jones et al (14 assays)
- Tissues - 9 Shen et al. (28 assays)
Hordeum vulgare subsp. vulgare
Macaca mulatta
Monodelphis domestica
Mus musculus
- Cell Types - 35 FANTOM5 project (122 assays)
- Cell Types - Cerebral cortex (17 assays)
- Cell Types - Developing heart (11 assays)
- Cell Types - Regulatory T cells - Krzyzanowska et al (12 assays)
- Cell Types - Six T cell subtypes (12 assays)
- Cell type - Cabezas-Wallscheid et al (16 assays)
- Cell type - Paulson et al (15 assays)
- Cell type - Soumillon et al (4 assays)
- Cell type - Wamstad et al (8 assays)
- Cell types - 3 Lienert et al (6 assays)
- Cell types - Capucha et al (14 assays)
- Cell types - Lavin et al (26 assays)
- Cells - hematopoetic stem and multipotent progenitor cells (20 assays)
- Circadian clock - Pembroke et al (54 assays)
- Developmental Stages - 5 (11 assays)
- Developmental Stages - DMDD mouse mutant lines (2660 assays)
- Developmental Stages - pure-bred wild-type embryos (DMDD) (16 assays)
- Developmental Stages - wild-type embryos (DMDD) (125 assays)
- Developmental Stages - wild-type embryos (DMDD) with het parentage (16 assays)
- Developmental stages - 4 (4 assays)
- Developmental stages - Schmitt et al (9 assays)
- Individuals - 258 Diversity Outbred (DO) mice (514 assays)
- Mernberger et al 2019 - Organism Part (9 assays)
- Sexes - brown adipose tissue - Visser et al (8 assays)
- Strains - 4 Bonthuis et al (86 assays)
- Strains - 4 Pfeiffer (4 assays)
- Strains - 8 Zheng et al (8 assays)
- Strains - Aitken et al., 2019 (7 assays)
- Strains - Gregg et al (203 assays)
- Sun et al., 2020 - Organism part (9 assays)
- Tissues - 14 (16 assays)
- Tissues - 2 (12 assays)
- Tissues - 3 (30 assays)
- Tissues - 3 Soumillon et al (7 assays)
- Tissues - 4 (10 assays)
- Tissues - 49 FANTOM5 project (248 assays)
- Tissues - 6 (36 assays)
- Tissues - 9 (9 assays)
- Tissues - 9 in 3 strains (26 assays)
- Tissues - Developing gut (6 assays)
- Tissues - Fat and muscle (9 assays)
- Tissues - GENCODE (8 assays)
- Tissues - Mammalian Kaessmann (20 assays)
- Tissues - Vertebrates (6 assays)
- Tissues, developmental stages - Mouse - Moreira et al (317 assays)
- Angelidis et al., 2019 - age - 24 month and 3 month (2 assays)
- Azimifar et al., 2014 - liver cell types (42 assays)
- Bundy et al. 2017 - sex (17 assays)
- Bundy et al., 2016 - Hippocampus, protocol (15 assays)
- Cell line - Menschaert et al (1 assays)
- Deshmukh et al., 2015 - organism part (6 assays)
- Duda et al., 2018 - organism part - brain regions (36 assays)
- Dudek et al., 2021 - sampling time points (6 assays)
- Hornburg et al., 2014 - cell lines (39 assays)
- Huttlin et al., 2010 - tissues - brain, heart, etc (8 assays)
- Jarrod et al., 2018 - tissue - retina (1 assays)
- Linscheid et al. 2019 - organism part (6 assays)
- Linscheid et al., 2021 - tissue - heart regions (4 assays)
- Meierhofer et al., 2016 - organism part (12 assays)
- Organism part - Geiger et al (27 assays)
- Organism part - Huttlin et al (9 assays)
- Organism part - Malmstrom et al (13 assays)
- Sarver DC et al., 2017 - Sex - female and male (8 assays)
- Schroeder et al., 2021 - developmental stage - juvenile and adult (6 assays)
- Zhao et al., 2019 - tissue - lens (1 assays)
Musa acuminata AAA Group
Oryctolagus cuniculus
Oryza sativa
Oryza sativa Japonica Group
- Huang et al 2017 - Root sampling sites (9 assays)
- Lee et al 2017 - Time (36 assays)
- Reynoso et al, 2018 - Fraction (8 assays)
- Tissues - 4 Zhang et al (4 assays)
- Tissues - 5 Hong et al.(2022) (14 assays)
- Tissues - 7 Sakai (28 assays)
- Tissues - 9 Davidson (11 assays)
- Tissues - Anderson et al (9 assays)
- Wang et al 2015 - Organism Part (single-end seq) (8 assays)
- Wang et al 2015 - Organism Parts (8 assays)
Papio anubis
Populus trichocarpa
Rattus norvegicus
- Ages - gastrocnemius muscle - Hoersch et al (57 assays)
- Ages - tibialis muscle - Hoersch et al (25 assays)
- Organism parts - tendons - Mendias et al (122 assays)
- Tissues - 11 Yu (659 assays)
- Tissues - 9 Merkin (20 assays)
- Tissues, developmental stages - Rat - Moreira et al (308 assays)
- Alugubelly N et al, 2019 - stimulus (6 assays)
- Huang Q et al, 2018 - compound, dose (12 assays)
- Limbutara K et al, 2020 - sampling site (32 assays)
- Roffia V et al, 2018 - treatment (20 assays)
- Thorpe CT et al., 2020 - tendon (3 assays)
- Venkatraman V et al, 2015 - ageing (12 assays)
- Vileigas DF et al, 2019 - diet (16 assays)
- Wisztorski et al., 2016 - spinal injury time series (80 assays)
Saccharomyces cerevisiae
Schistosoma mansoni
Setaria italica
Solanum lycopersicum
Solanum tuberosum
Sorghum bicolor
- Emms et al., 2016 - Cell type (6 assays)
- Kebrom et al 2017 - Sampling site (12 assays)
- Thurber et al., 2015 - Organism part (4 assays)
- Tissues - 3 Makita et al. (9 assays)
- Tissues - Davidson et al (10 assays)
- Tissues - Olson et al (17 assays)
- Turco et al 2017 - Organism Part (12 assays)
- Wang et al., 2018 - Organism part (165 assays)
Sus scrofa
- Developmental stages - 8, 10 and 12 day embryos (30 assays)
- Tissues - The Roslin Institute (301 assays)
- Pig2023_Tissue - heart - Hinrichs et al. 2021 (8 assays)
- Pig2023_Tissue - liver - Backman et al. 2019 (5 assays)
- Pig2023_Tissue - liver - Riedel et al. 2020 (8 assays)
- Pig2023_Tissue - retina - Cehofski et al. 2015 (16 assays)
- Pig2023_Tissue - retina - Schmelter et al. 2018 (12 assays)
- Pig2023_Tissues - Marx H et al. 2017 (9 assays)
- Pig2023_Tissues - adipose - Frohlich et al. 2023 (10 assays)
- Pig2023_Tissues - biceps femoris- Fröhlich T et al. 2016 (6 assays)
- Pig2023_Tissues - biceps, triceps - Moretti et al. 2020 (4 assays)
- Pig2023_Tissues - biceps, triceps - Regensburger et al. 2019 (4 assays)
- Pig2023_Tissues - gastrointestinal tract - Tröscher-MuÃotter et al. 2019 (16 assays)
- Pig2023_Tissues - heart atrium, ventricle - Linscheid et al. 2021 (4 assays)
- Pig2023_Tissues - heart, muscle - Wolf et al. 2023 (20 assays)
- Pig2023_Tissues - heart- Federspiel JD et al. 2019 (6 assays)
Theobroma cacao
Trifolium pratense
Triticum aestivum
Vitis vinifera
- Bagnaresi et al., 2020 - Cultivar (18 assays)
- Cramer et al., 2015 - Cultivar (84 assays)
- Cultivars - 10 Potenza et al (9 assays)
- Cultivars - 5 Palumbo et al. (60 assays)
- Da Silva et al., 2013 - Organism part (11 assays)
- Dal Santo et al 2018 - Cultivar (72 assays)
- Leaf development - Pervaiz et al (4 assays)
- Massonnet et al., 2019 - Developmental stage (16 assays)
- Tissues - Venturini et al (9 assays)
- Wang et al, 2019 - Developmental stage (12 assays)
Xenopus tropicalis
Zea mays
- Cell Type - Nelson et al 2014 (12 assays)
- Cell Types - Seed Lloyd et al (4 assays)
- Chen et al., 2017 - Cell types (18 assays)
- Cruz et al., 2020 - Individual (92 assays)
- Cultivar - 2 inbred Regulski (6 assays)
- Cultivars - eight inbred lines (3 assays)
- Frey et al, 2015 - Cultivar (51 assays)
- Huang et al 2017 - Root sampling site (9 assays)
- Koch et al, 2016 - Organism part (12 assays)
- Lemmon et al, 2014 - Cultivar (440 assays)
- Meng et al, 2017 - Age (24 assays)
- Oka et al, 2017 - Sampling site (18 assays)
- Organism Part - Chang et al 2012 (4 assays)
- Pang et al., 2018 - Cultivar (291 assays)
- Reyes et al, 2017 - Cell type (8 assays)
- Sampling Time Points - Plant Systems Biology Uni Ghent (16 assays)
- Sampling sites - Li et al 2010 (12 assays)
- Seed development - Chen et al (65 assays)
- Seifert et al., 2018 - Cultivar (25 assays)
- Shuai Wang et al, 2014 - Organism part (6 assays)
- Thatcher et al., 2014 - Cultivar (94 assays)
- Tissues - 4 Chettoor et al (11 assays)
- Tissues - 5 Xu et al (5 assays)
- Tissues - 6 Wang (36 assays)
- Tissues - Stelpflug et al (267 assays)
- Tissues - Walley et al (68 assays)
- Wang et al 2014 - Sampling site (75 assays)
- Wang et al, 2018 - Cultivar (14 assays)
- Wang et al., 2018 - Organism part (36 assays)
- Want et al., 2020 - Cultivar (40 assays)