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Unknown (3867)
Genomics (2401)
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Proteomics (103)
Other (65)
Methylation profiling (58)
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Organisms

Mus musculus (1594)
Homo sapiens (680)
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synthetic construct (2)
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Mus musculus musculus x Mus musculus castaneus (1)
Pyricularia oryzae (1)
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human gammaherpesvirus 4 (1)
JC polyomavirus (1)
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Betapolyomavirus hominis (1)
Human alphaherpesvirus 2 (1)

Organisms

Mus musculus (1096)
Homo sapiens (315)
human gut metagenome (57)
Macaca mulatta (11)
Rattus norvegicus (9)
Equus caballus (8)
Drosophila melanogaster (5)
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Papio anubis (3)
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Ictalurus punctatus (2)
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Mus musculus musculus (2)
Mus (2)
Edwardsiella ictaluri ATCC 33202 (1)
Mus musculus musculus x Mus musculus castaneus (1)
Pseudomonas savastanoi pv. nerii (1)
Eucalyptus tereticornis (1)
Edwardsiella phage eiAU (1)
Edwardsiella ictaluri (1)
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Repository

ENA (1745)
geo (1134)
biostudies-arrayexpress (1054)
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pride (83)
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Tissue

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Disease

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Not applicable (1)
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Technology Type

Mass Spectrometry (83)
Shotgun proteomics (44)
Affinity purification coupled with mass spectrometry proteomics (35)
Gel-based experiment (6)
Data-dependent acquisition (5)
Illumina HiSeq 2000 (4)
Bottom-up proteomics (4)
Illumina (3)
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Chemical cross-linking coupled with mass spectrometry proteomics (2)
Data-independent acquisition (2)
Illumina_Infinium_HumanMethylation450, Illumina_HumanHT-12v4 (1)
Illumina MiSeq (1)
Affinity proteomics (1)
All-ion fragmentation (1)
DiaPASEF (1)
SRM/MRM (1)
SWATH MS (1)
Top-down proteomics (1)

Instrument Platform

Illumina HiSeq 2000 (29)
NextSeq 500 (29)
Illumina NovaSeq 6000 (18)
Illumina HiSeq 2500 (17)
Illumina HiSeq 4000 (15)
Illumina Genome Analyzer IIx (8)
Illumina HiSeq 1000 (4)
Q Exactive Plus (4)
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None (3)
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Orbitrap Exploris 480 (3)
NextSeq 2000 (2)
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DELL PRECISION T7500 (1)
DELL PRICISION T7500 (1)
DELL PRECISION 7500 (1)
Not (1)
Agilent DNA Microarray Scanner Model #G2565BA (1)
Fluidigm C1 (1)
Linux computer (1)
Linux Beowulf cluster; AMD Opteron Linux Beowulf cluster; AMD Opteron 6168 (1)
Agilent 2100 Bioanalyzer (1)
GenePix 4000B [Axon Instruments] (1)
Scanning hardware (1)
Affymetrix Fluidics Station 400 (1)
N/a (1)
Illumina HiSeq 3000 (1)

Publication Date

2014 (222)
2013 (214)
2015 (199)
2016 (196)
2012 (150)
2011 (134)
2023 (127)
2018 (107)
2020 (106)
2010 (104)
2022 (103)
2025 (97)
2017 (92)
2024 (87)
2021 (87)
2019 (77)
2026 (70)
2009 (58)
2008 (30)
2007 (21)
2006 (7)
2005 (3)
2004 (1)
2002 (1)

UNIPROT ID/AC

A0A5E1 (1)
A0ELI5 (1)
A0EQY3 (1)
A0JLQ7 (1)
A0JNY3 (1)
A0JNY7 (1)
A0MNP4 (1)
A0PJD7 (1)
A0PJL0 (1)
A0PK78 (1)
A0PK81 (1)
A1A553 (1)
A1A557 (1)
A1A558 (1)
A1A596 (1)
A1A5B6 (1)
A1E5T5 (1)
A1ILG8 (1)
A1L013 (1)
A1L0U3 (1)
A1L0U6 (1)
A1L0V6 (1)
A1L317 (1)
A1L329 (1)
A1L341 (1)
A1L347 (1)
A1L353 (1)
A1L361 (1)
A1L366 (1)
A1L3B6 (1)

ENSEMBL ID

ENSMUSG00000021039 (1)
ENSMUSG00000027651 (1)
ENSMUSG00000098557 (1)
ENSMUSP00000069525 (1)
ENSMUSP00000140201 (1)
ENSMUSP00000141097 (1)
ENSMUSP00000141637 (1)

CHEBI ID

CHEBI:17822 (3)
CHEBI:18257 (3)
CHEBI:25017 (3)
CHEBI:17148 (3)
CHEBI:16610 (3)
CHEBI:37024 (3)
CHEBI:9330 (2)
CHEBI:165867 (2)
CHEBI:60647 (2)
CHEBI:45892 (2)
CHEBI:16077 (2)
CHEBI:31252 (2)
CHEBI:17768 (2)
CHEBI:24149 (2)
CHEBI:86542 (2)
CHEBI:32365 (2)
CHEBI:29888 (2)
CHEBI:36090 (2)
CHEBI:33569 (2)
CHEBI:17200 (2)
CHEBI:17553 (2)
CHEBI:21563 (2)
CHEBI:36751 (2)
CHEBI:46961 (2)
CHEBI:16543 (2)
CHEBI:17256 (2)
CHEBI:23673 (2)
CHEBI:16264 (2)
CHEBI:17363 (2)
CHEBI:26271 (2)

Metabolite Name

Aminoadipic acid (2)
Proline (2)
Methionine (2)
Choline (2)
Creatine (2)
Valine (2)
Putrescine (2)
Spermidine (2)
7-methylguanine (2)
1-methyladenosine (2)
2-hydroxycinnamic acid (2)
6-phosphogluconic acid (2)
2-hydroxyundecanoate (1)
2,4-dihydroxybenzaldehyde (1)
5alpha-cholestanol (1)
(4-hydroxy-3-methoxyphenyl)ethanol (1)
D-maltose (1)
5,7-dihydroxy-4'-methoxyisoflavone (1)
Cholesterone (1)
Delta-tocopherol (1)
3,4-dihydroxyphenylvaleric acid (1)
2',6'-dihydroxyacetophenone (1)
Myo-inositol phosphate (1)
Triacontanol (1)
2,4,6-trihydroxybenzoic acid (1)
Glycero-d-gulo-heptose (1)
2-amino-7,10-dimethyldibenzo[b,f][1,4]oxazepin-11(10h)-one (1)
D-fructose-1-phosphate (1)
1,4-dihydroxy-2,6-dimethoxybenzene (1)
N'-(1h-indol-3-ylmethylene)benzohydrazide (1)

First Public Date

2014 (325)
2024 (154)
2023 (146)
2025 (126)
2022 (114)
2019 (113)
2017 (112)
2020 (111)
2018 (111)
2021 (109)
2026 (103)
2015 (81)
2013 (70)
2016 (69)
2012 (1)

Study status

Completed (1)

Lab affiliation

1. Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel 2. Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel (3)
Center for Genomic Regulation Differentiation and Cancer Passeig Maritim 37-49 Barcelona 08003 SPAIN (2)
Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands (2)
Ottawa Hospital Research Institute (2)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark (2)
-Associate Research Professor, Institut de recherches cliniques de Montréal (IRCM), RNP Biochemistry laboratory -Professeure agrégée, Département de biochimie et médecine moléculaire, Université de Montréal -Associate Professor, Division of Experimental Medicine, McGill University (1)
1. Competence Centre on Health Technologies, Tiigi 61b, Tartu, Estonia 2. Chair of Obstetrics and Gynaecology, Institute of Biomedicine, University of Tartu, Ravila 19, Tartu, Estonia (1)
1. Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel. 2. Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel. (1)
Asan Medical Center, Clinical Proteomics Core, Republic of Korea (1)
Associate Professor, Center for Genomics and Systems Biology, Dept of Biology, New York University (1)
Babraham Institute (1)
Babraham Istitute (1)
Babraham Research Campus, Cambridge, UK (1)
Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China (1)
CRG, UPF (1)
Cell Fate Engineering and Therapeutics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore (1)
Cell and Chemical Biology Leiden University Medical Center (1)
Cell and Regenerative Biology, University of Wisconsin-Madison (1)
Center for Genomic Regulation (CRG) University Pompeu Fabra (UPF) (1)
Centre for Genomic Regulation (CRG), Barcelona, Spain (1)
DNA damage responses and cancer lab Department of Human Genetics Leiden University Medical Center Eithovenweg 20 2333ZC Leiden The Netherlands (1)
Department of Anatomy and Developmental Biology, Australian Regenerative Medicine Institute, Monash University, Australia (1)
Department of Biochemistry, University of Cambridge (1)
Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany (1)
Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy. (1)
Department of Convergence Medicine, Convergence Medicine Research Center/Biomedical Research Center, Asan Medical Center, Asan Institute for Life Sciences, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea. (1)
Department of Genom Regulation Friedrich Miescher Institute for Biomedical Research Maulbeerstr. 66 4058 Basel Switzerland (1)
Department of Genome Regulation Friedrich Miescher Institute for Biomedical Research Maulbeerstr. 66 4058 Basel Switzerland (1)
Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal (1)
Department of Medicine, Columbia University Irving Medical Center (1)

Keyword

BRAF Class 3 (1)
NF1 LOF (1)
KRAS amplification (1)
KRAS mutations (1)
Neoplasm, squamous cell (1)
Esophageal neoplasms carcinoma, bronchogenic (1)
Thoracic neoplasms (1)
Endometrium/uterus cancer (1)
KRAS G12 (1)
Advanced solid malignancies (1)
Bronchial neoplasms (1)
Respiratory tract neoplasms (1)
Neoplasms by site (1)
PTPN11 (1)
Osimertinib (1)
SHP2 (1)
Respiratory tract diseases (1)
Skin cancer (1)

Classification

bacteria (3)
fungi (1)
viruses (1)

Modification

2x(15)N labeled L-lysine (1)
4 (1)
4x(15)N labeled L-arginine (1)
N6 (1)

Study type

Transcription profiling by array (476)
RNA-seq of coding RNA (186)
ChIP-seq (184)
Methylation profiling by high throughput sequencing (27)
Other (24)
Methylation profiling by array (22)
RNA-seq of coding RNA from single cells (19)
Comparative genomic hybridization by array (16)
RNA-seq of non coding RNA (15)
ChIP-chip by tiling array (14)
ATAC-seq (10)
Cell line - High-throughput sequencing (9)
RNA-seq of total RNA (8)
Unknown experiment type (6)
DNA-seq (6)
Genotyping by array (5)
ChIP-chip by array (4)
Hi-C (3)
MicroRNA profiling by array (3)
GRO-seq (2)
High-throughput sequencing (2)
RNAi profiling by array (2)
Transcription profiling by RT-PCR (2)
FAIRE-seq (1)
Transcription profiling by SAGE (1)
Differential (1)
Animal - Single-cell sequencing (1)
Trajectory (1)
Proteomic profiling by mass spectrometer (1)
Transcription profiling by tiling array (1)

Release Date

2022 (500)
2021 (493)
2020 (436)
2023 (435)
2024 (416)
2025 (410)
2014 (268)
2015 (261)
2016 (238)
2013 (233)
2019 (199)
2018 (189)
2012 (186)
2017 (167)
2011 (165)
2010 (124)
2009 (77)
2026 (38)
2008 (38)
2007 (29)
2005 (7)
2006 (6)
2004 (2)
2002 (2)
2003 (1)

Location

South Korea (1)
United States (1)

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KDM6 Inhibition induces DNA Damage Response (DDR) during ESC Differentiation but not during self-renewal.

The discovery of the first histone demethylase in 2004 (LSD1/KDM1) opened new avenues for the understanding of how histone methylation impacts cellular functions. A great number of histone demethylases have been identified since, which are potentially linked to gene regulation as well as to stem cel...

ORGANISM(S): Mus musculus

2016-03-11 | E-GEOD-49886 | biostudies-arrayexpress

Identification of differential expressed genes between P-RPCs, ESC-RPCs and Dkk1 treated ESC-RPCs through genome-wide transcript profiling

Tumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide...

ORGANISM(S): Mus musculus

2013-04-16 | E-GEOD-34002 | biostudies-arrayexpress

Polycomb protein EED is required for selective silencing of pluripotency genes upon ESC differentiation

Eed (embryonic ectoderm development) is a core component of the Polycomb Repressive Complex 2 (PRC2) which catalyzes the methylation of histone H3 lysine 27 (H3K27). Trimethylated H3K27 (H3K27me3) can act as a signal for PRC1 recruitment in the process of gene silencing and chromatin condensation. P...

ORGANISM(S): Mus musculus

2014-08-28 | E-GEOD-49305 | biostudies-arrayexpress

PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation (RRBS)

Polycomb Repressive Complex 2 (PRC2) catalyzes histone H3 lysine 27 tri-methylation, an epigenetic modification associated with gene repression. H3K27me3 is enriched at the promoters of a large cohort of developmental genes in embryonic stem cells (ESCs). Loss of H3K27me3 leads to a failure of ESCs ...

ORGANISM(S): Mus musculus

2014-11-17 | E-GEOD-53507 | biostudies-arrayexpress

PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation (RNA-Seq)

ORGANISM(S): Mus musculus

2014-11-17 | E-GEOD-53506 | biostudies-arrayexpress

PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation (ChIP-Seq)

ORGANISM(S): Mus musculus

2014-11-17 | E-GEOD-53505 | biostudies-arrayexpress

Histone Variant H2A.X Plays Novel Roles in Cell Lineage Commitment and Genomic Stability in ESC and iPSC

Herein, we demonstrated that the cell lineage commitment is unexpectedly regulated by the novel functions of H2A.X, a histone variant which was only well-known for its role in genome integrity maintenance previously. Surprisingly, only in ESCs but not differentiated cells, H2A.X is specifically targ...

ORGANISM(S): Mus musculus

2014-09-07 | E-GEOD-49147 | biostudies-arrayexpress

INO80 complex in the core regulatory network governing ESC self-renewal [ChIP-Seq]

Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains ...

ORGANISM(S): Mus musculus

2014-05-16 | E-GEOD-49137 | biostudies-arrayexpress

Capitella teleta strain:I ESC-2004

Capitella teleta I ESC-2004 transcriptome - Capsp_L1

PRJNA584476 | ENA

Capitella teleta strain:I ESC-2004

Capitella teleta I ESC-2004 transcriptome - Capsp_L2

PRJNA584478 | ENA

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