Embryonic bodies

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Transcriptomics (659)
Unknown (657)
Genomics (641)
Proteomics (59)
Methylation profiling (17)
Other (15)
Metabolomics (8)
Models (1)

Organisms

Mus musculus (549)
Homo sapiens (269)
Schizosaccharomyces pombe (33)
Human immunodeficiency virus 1 (33)
Oryza sativa Indica Group (33)
Sinorhizobium meliloti BL225C (33)
Sus scrofa domesticus (33)
Ostreococcus tauri (33)
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synthetic construct (4)
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Mammalia (1)
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cellular organisms (1)

Organisms

Mus musculus (319)
Homo sapiens (70)
Drosophila melanogaster (11)
Caenorhabditis elegans (3)
Sus scrofa (3)
Rattus norvegicus (3)
Gallus gallus (3)
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Danio rerio (1)
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Repository

biostudies-arrayexpress (565)
ENA (465)
geo (296)
pride (33)
MassIVE (17)
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jPOST (6)
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ExpressionAtlas (3)
PanoramaPublic (2)
BioModels (1)
iProX (1)

Tissue

Embryonic stem cell (15)
Cell culture (13)
Early embryonic cell (4)
Cell suspension culture (4)
Stem cell (3)
Fibroblast (3)
Hepatocyte (2)
Embryonic kidney cell line (2)
Epithelial cell (2)
Dermomyotome (1)
Myotome (1)
Trunk somite (1)
Paraxial mesoderm (1)
Stem cell differentiation (1)
Mesoderm (1)
Endometrial gland (1)
Neuron of cerebral cortex (1)
Retina (1)
Keratinocyte (1)
Leukocyte (1)
Macrophage (1)
Multipotent stem cell (1)
Brain (1)
Embryo (1)
Spleen (1)
B cell (1)
Monocyte (1)
T cell (1)

Disease

Disease free (3)
Cocaine addiction (1)
Normal (1)
Female infertility (1)
Colon cancer (1)

Technology Type

Mass Spectrometry (33)
Shotgun proteomics (18)
Affinity purification coupled with mass spectrometry proteomics (8)
Bottom-up proteomics (6)
Mass spectrometry (5)
Gel-based experiment (3)
Data-dependent acquisition (3)
Mass spectrometry assay (2)
Data-independent acquisition (2)
Combined on identical nucleotide universal identifier, Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip (1)
NMR spectroscopy (1)
SWATH MS (1)

Instrument Platform

Illumina NovaSeq 6000 (29)
Illumina HiSeq 4000 (19)
NextSeq 500 (17)
Illumina HiSeq 2500 (9)
Illumina NovaSeq X (5)
Illumina HiSeq 2000 (5)
Illumina Genome Analyzer II (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
DNBSEQ-G400 (2)
NextSeq 550 (2)
Chromium X instrument (10x Genomics); GEM-X FX Chips (10x Genomics); Agilent TapeStation D1000; qPCR (library quantification kit for Illumina platforms) (1)
Chromium X instrument (10x Genomics); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781); Human Gene Expression Probe Set v1.0.1 (10x Genomics) (1)
Countess 3 FL Automated Cell Counter (Thermo Fisher Scientific; AMQAF2000); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781) (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
Chromium Next GEM Chip G (1)
10X v3 (1)
Single nuclei were captured using the 10x Genomics Chromium Controller. (1)
Cutadapt, STAR (1)
TruSeq Stranded mRNA Sample Prep Kit (Illumina) (1)
BD InFlux Cytometer (Becton-Dickinson) (1)
Not (1)
Agilent DNA Microarray Scanner Model #G2565BA (1)
Fluidigm C1 (1)
None (1)
Agilent 2100 Bioanalyzer (1)
G2565AA DNA microarray scanner [Agilent] (1)
Illumina Genome Analyzer IIx (1)
Affymetrix Fluidics Station 400 (1)

Publication Date

2015 (89)
2014 (85)
2012 (75)
2016 (69)
2013 (69)
2011 (64)
2025 (57)
2010 (48)
2026 (40)
2020 (40)
2024 (36)
2023 (34)
2021 (34)
2009 (31)
2022 (29)
2018 (29)
2008 (29)
2017 (25)
2019 (21)
2007 (13)
2005 (9)
2006 (3)
2004 (3)

CHEBI ID

CHEBI:15422 (2)
CHEBI:16977 (2)
CHEBI:15428 (2)
CHEBI:17268 (2)
CHEBI:17203 (2)
CHEBI:15891 (2)
CHEBI:16737 (2)
CHEBI:16414 (2)
CHEBI:17191 (2)
CHEBI:15724 (2)
CHEBI:15603 (2)
CHEBI:16643 (2)
CHEBI:75195 (1)
CHEBI:138553 (1)
CHEBI:138554 (1)
CHEBI:74240 (1)
CHEBI:72072 (1)
CHEBI:72076 (1)
CHEBI:91073 (1)
CHEBI:72065 (1)
CHEBI:72059 (1)
CHEBI:143617 (1)
CHEBI:143618 (1)
CHEBI:91065 (1)
CHEBI:72064 (1)
CHEBI:138909 (1)
CHEBI:74375 (1)
CHEBI:72058 (1)
CHEBI:72087 (1)
CHEBI:72086 (1)

Metabolite Name

Adenosine (3)
(2,6-Dihydroxy-4-methoxyphenyl)(4-hydroxy-2-methoxy-6-methylphenyl)methanone (2)
13-Hydroxy-6-(1-hydroxyethyl)-12,14-dimethyl-3-methylidene-15-nonyl-9-(propan-2-yl)-1-oxa-4,7,10-triazacyclopentadecane-2,5,8,11-tetrone (2)
3-(4-Hydroxy-2,2-dimethyl-1-oxo-3,3a-dihydroimidazo[1,2-a]indol-4-yl)-2-(4-oxoquinazolin-3-yl)propanoic acid (2)
5-Amino-2-(3,4'-dihydroxy-4,4,7,8a-tetramethyl-6'-oxospiro[2,3,4a,5,6,7-hexahydro-1H-naphthalene-8,2'-3,8-dihydrofuro[2,3-e]isoindole]-7'-yl)-5-oxopentanoic acid (2)
Ala-Gly-Arg (2)
Dye X-26647-194 (2)
Dye X-5380-16 Cation (2)
Griseophenone B (2)
N-((7E,11Z)-6,13,14-Trihydroxy-3-(1H-indol-3-ylmethyl)-4,5,10,12-tetramethyl-1,17-dioxo-2,3,3a,6,6a,9,10,13,14,15,16,17-dodecahydro-1H-cyclotrideca[d]isoindol-15-yl)acetamide (2)
N-[(1E)-2-(4-Nitrophenyl)-1-azavinyl]-2-(2-naphthylamino)acetamide (2)
N5-(1-Imino-3-butenyl)-L-ornithine (2)
N5-(1-Iminobutyl)-L-ornithine (2)
Oleana-1,9(11)-dien-28-amide, 2-cyano-3,12-dioxo-N-(2,2,2-trifluoroethyl)- (2)
[(2R,3R,4S,5S,6R)-2-(Acetyloxymethyl)-5-hexanoyloxy-3-hydroxy-6-[(2S,3R)-2,3,4-trihydroxybutoxy]oxan-4-yl] tetradecanoate (2)
[(4S,6R,6aS,9R,10S)-6,10-Diacetyloxy-6a,9-dihydroxy-3-(methoxymethyl)-6,9-dimethyl-2-oxo-5,7,8,10-tetrahydro-4H-benzo[h][1]benzofuran-4-yl] 2-methylprop-2-enoate (2)
2-{2-[2-(Methacryloyloxy)ethoxy]ethoxy}ethyl 2-methylacrylate (2)
N-Arachidonoyltaurine (2)
3-Quinolinecarboxamide, 1,4-dihydro-8-methoxy-4-oxo-1-pentyl-N-tricyclo[3.3.1.13,7]dec-1-yl- (2)
N-(adamtan-1-yl)-1-pentyl-1H-indole-3-carboxamide (2)
1H-Indole-4-carboxamide, N-[(1,2-dihydro-4,6-dimethyl-2-oxo-3-pyridinyl)methyl]-3-methyl-1-[(1S)-1-methylpropyl]-6-[6-(1-piperazinyl)-3-pyridinyl]- (2)
2-[(1-Methyl-1H-tetraazol-5-yl)sulfanyl]-N-(2-phenylethyl)acetamide (2)
N-Benzyl(1-naphthyl)methanamine (2)
[4-Anilino-2-(4-fluorophenyl)-5-oxo-1-phenyl-2,5-dihydro-1H-pyrrol-3-yl]acetic acid (2)
Desferrichrome (2)
1H-Indazole-3-carboxamide, N-[1-(aminocarbonyl)-2,2-dimethylpropyl]-1-pentyl- (2)
1-(Benzoyloxy)propan-2-yl benzoate (2)
6-Bromo-4-(piperazin-1-yl)quinazoline (2)
Sebacic acid bis(N-succinimidyl) ester (2)
(-)-Secoisolariciresinol (2)

IsPrivate

False (1)

Model Flag

Non Kinetic (1)

First Public Date

2014 (96)
2024 (45)
2025 (42)
2019 (34)
2020 (32)
2026 (29)
2023 (29)
2017 (29)
2015 (27)
2022 (26)
2013 (21)
2021 (20)
2016 (18)
2018 (16)
2011 (1)

Study type

Transcription profiling by array (257)
RNA-seq of coding RNA (101)
ChIP-seq (77)
RNA-seq of coding RNA from single cells (32)
Methylation profiling by high throughput sequencing (19)
Methylation profiling by array (12)
Other (8)
Comparative genomic hybridization by array (7)
ChIP-chip by tiling array (6)
RNA-seq of non coding RNA (6)
Unknown experiment type (5)
Transcription profiling by tiling array (4)
ATAC-seq (4)
MicroRNA profiling by array (3)
RNA-seq of total RNA (3)
Transcription profiling by SAGE (2)
Cell line - Single-cell sequencing (2)
Cell line - High-throughput sequencing (2)
ChIP-chip by array (2)
MeDIP-seq (1)
Cell line - One-color microarray (1)
Translation profiling (1)
High-throughput sequencing (1)
Genotyping by array (1)
MBD-seq (1)
Transcription profiling by RT-PCR (1)
Bisulfite-seq (1)
ScATAC-seq (1)
Single nucleus RNA sequencing (1)
DNA-seq (1)

Release Date

2014 (118)
2015 (112)
2012 (110)
2013 (97)
2016 (92)
2011 (80)
2010 (67)
2021 (53)
2017 (53)
2022 (48)
2020 (47)
2025 (45)
2009 (44)
2023 (41)
2018 (40)
2008 (40)
2019 (28)
2024 (27)
2026 (24)
2007 (21)
2006 (12)
2005 (9)
2004 (4)
2000 (3)
1998 (3)
1999 (2)
2002 (1)
2001 (1)

Lab affiliation

Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands Division of Molecular Genetics, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands (2)
Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), 100, Plastira Str., 70013 Heraklion, Crete, Greece. (2)
Max Delbrück Center for Molecular Medicine in the Helmholtz Association (2)
Department of Medicine, Cardiology division, Lillehei Heart Institute, University of Minnesota, USA (1)
Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, United States (1)
The Wilmer Eye Institute, Johns Hopkins University Schoolof Medicine, Baltimore, Maryland 21287 USA (1)
Medical Research Council - London Institute of Medical Sciences, Telomere Replication and Stability Group, United Kingdom. (1)
Cellular and Molecular Pathology, UCSF (1)
Cell and Chemical Biology Leiden University Medical Center Leiden The Netherlands (1)
Lab of Neuroproteomics, Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, Brazil (1)
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China (1)
Center of Growth Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, China. (1)
Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (1)
Group “Retinal degeneration and regeneration” Department of Ophthalmology University of Lausanne Hôpital Ophtalmique Jules-Gonin Fundamental research center 15 av. de France 1004 Lausanne Switzerland (1)
Department of Biology, Southern University of Science and Technology, China (1)
Professor and Chair of Chemical Biology, Peking-Tsinghua Center for Life Sciences Peking University, Beijing, China. Associate Editor, ACS Chemical Biology (1)
Research Group Leader Bulut-Karslioglu lab Dept. of Genome Regulation Max Planck Institute for Molecular Genetics Ihnestrasse 63-73 14195 Berlin GERMANY (1)
Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan, Republic of China (1)
dana farber cancer institute and harvard medical school (1)
IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China (1)
Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) Beutenbergstr. 11 07745 Jena Germany Tel.: +49-3641-656831 (1)
Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet SE 17177 Stockholm, Sweden. Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia. (1)
German Cancer Research Center (1)
Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea (1)
Department of Obstetrics and Gynecology, School of Medicine, Stanford University, CA, USA. Igenomix Foundation, Instituto de Investigación Sanitaria Hospital Clínico (INCLIVA), Valencia, Spain (1)
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands (1)
Cell and Chemical Biology Leiden University Medical Center (1)
Proteomic Facility, Institut Jacques Monod, UMR7592 (CNRS and Paris University) (1)
Cell and Chemical Biology Leiden University Medical Center The Netherlands (1)
Head of the Curie Institute Mass Spectrometry Platform (1)

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1H NMR metabolite monitoring during the differentiation of human induced pluripotent stem cells provides new insights into the molecular events that regulate embryonic chondrogenesis

The integration of cell metabolism with signalling pathways, transcription factor networks and epigenetic mediators is critical in coordinating molecular and cellular events during embryogenesis. Induced pluripotent stem cells (IPSCs) are an established model for embryogenesis, germ layer specificat...

2023-05-24 | MTBLS4854 | MetaboLights

Short-term (12h) ATRA treatment of embryoid bodies.

We used microarrays to detail the global programme of gene expression in embryonic stem cells, early differentiated embrioid bodies and effect of short-term ATRA treatment. Expression data from undifferentiated mouse embryonic stem cells (D3), four-day old aggregated embrioid bodies and 12h atRA or ...

ORGANISM(S): Mus musculus

2010-07-16 | E-GEOD-20919 | biostudies-arrayexpress

Transcription profiling of mouse embryonic stem cells (ESCs) differentiation into embyroid bodies (EBs

Stem cell differentiation is known to involve changes in RNA expression, but little is known about translational control during differentiation. We comprehensively profiled gene expression during differentiation of embryonic stem cells (ESCs) into embyroid bodies (EBs) by integrating conventional t...

ORGANISM(S): Mus musculus

2008-06-20 | E-GEOD-9563 | biostudies-arrayexpress

Expression data from wild type and globally hypomethylated mouse embryonic stem cells (ESCs) during their differentiation as embyroid bodies

To analyze the role of DNA methylation during differentiation, we performed genome-wide expression analysis of undifferentiated wild type, dnmt1-/- and triple knock out (TKO; dnmt1-/-, dnmt3a-/-, dnmt3b-/-) ESCs as well as respective embryoid bodies (EBs) at two stages of differentiation We generate...

ORGANISM(S): Mus musculus

2013-02-05 | E-GEOD-36679 | biostudies-arrayexpress

5-hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.

Hydroxymethylcytosine (5hmC) was recently found to be abundantly present in certain cell types including embryonic stem cells. The function of 5hmC is poorly understood. Here we have generated a genome-wide map of 5hmC in human embryonic stem cells (hESCs) by hydroxymethyl-DNA immunoprecipitation fo...

ORGANISM(S): Homo sapiens

2011-06-13 | E-GEOD-27627 | biostudies-arrayexpress

Transcription profiling of human embryonic stem (ES) cells. Undifferentiated cells of different passage numbers (p19 and p128) were vs cells differentiated in hanging drops for 5 days (d5 embryoid bodies) or expanded on gelatin coated dishes for a further 9 days (d14 embryoid bodies)

Undifferentiated cells of different passage numbers (p19 and p128) were compared to cells differentiated in hanging drops for 5 days (d5 embryoid bodies) or expanded on gelatin coated dishes for a further 9 days (d14 embryoid bodies).

ORGANISM(S): Homo sapiens

2005-08-31 | E-MEXP-303 | biostudies-arrayexpress

FunGenES: FunGenES_UKOE-5: Transcriptional profiling of CD31(+) cells isolated from murine embryonic stem cells

This experiment is part of the FunGenES project (FunGenES - Functional Genomics in Embryonic Stem Cells partially funded by the 6th Framework Programme of the European Union, http://www.fungenes.org). The experiment was conducted at University of Cologne, Cologne, Germany. Goal of the experiment is ...

ORGANISM(S): Mus musculus

2011-02-25 | E-TABM-1125 | biostudies-arrayexpress

Transcription profiling of murine V6.5 embryonic stem cells differentiating into embryoid bodies over a time-course to study changes in transcription during stem cell differentiation

An 11-point time course study comparing V6.5 embryonic stem cells versus embryoid bodies. Time course 0 hours, 6 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 4 days, 7 days, 9 days, and 14 days. Experiment Overall Design: this experiment include 11 samples and 66 replicates

ORGANISM(S): Mus musculus

2007-12-18 | E-GEOD-3231 | biostudies-arrayexpress

Transcription profiling of murine R1 embryonic stem cells differentiating into embryoid bodies over a time-course to study changes in transcription during stem cell differentiation

An 11-point time course study comparing R1 embryonic stem cells versus embryoid bodies. Time course 0 hours, 6 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 4 days, 7 days, 9 days, and 14 days. Experiment Overall Design: this experiment include 11 samples and 66 replicates

ORGANISM(S): Mus musculus

2007-11-16 | E-GEOD-2972 | biostudies-arrayexpress

Transcription profiling to compare embryonic stem cells, embryoid bodies and blast cells to breast epithelial, leuckocytes, endothelial and stromal cells (GEO Super Series)

This SuperSeries is composed of the following subset Series:; GSE8884: Expression data from human embryonic stem cells, early stage embryoid bodies, and hES-derived blast cells. GSE9086: Reanalysis of GSE8884 Samples with Breast Epithelial Samples from GSE3744. GSE9089: Reanalysis of GSE8884 Samples...

ORGANISM(S): Homo sapiens

2008-06-17 | E-GEOD-9196 | biostudies-arrayexpress

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