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Unknown (62817)
Genomics (6144)
Transcriptomics (3901)
Proteomics (626)
Metabolomics (173)
Other (34)
Models (21)
Methylation profiling (18)
Genomic (8)
Multiomics (6)

Organisms

Homo sapiens (1240)
Mus musculus (798)
Caenorhabditis elegans (485)
Arabidopsis thaliana (276)
Drosophila melanogaster (214)
Saccharomyces cerevisiae (88)
Danio rerio (80)
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Medicago truncatula (13)
Campylobacter jejuni (13)
Oryza sativa Indica Group (13)
Macaca mulatta (12)
Canis lupus familiaris (8)
Felis catus (3)

Organisms

Mus musculus (1512)
Homo sapiens (960)
Arabidopsis thaliana (370)
Drosophila melanogaster (237)
Caenorhabditis elegans (165)
Danio rerio (161)
Oryza sativa (69)
Gallus gallus (50)
Glycine max (43)
Zea mays (43)
Xenopus laevis (38)
Rattus norvegicus (38)
Xenopus tropicalis (32)
Saccharomyces cerevisiae (29)
Bos taurus (22)
Solanum lycopersicum (21)
Plasmodium falciparum (20)
Triticum aestivum (19)
Oryza sativa Japonica Group (15)
Strongylocentrotus purpuratus (14)
Harpegnathos saltator (13)
Pristionchus pacificus (13)
Anopheles gambiae (13)
Macaca mulatta (13)
Oryza sativa Indica Group (11)
Sus scrofa (11)
Vitis vinifera (11)
unidentified (10)
Neurospora crassa (9)
Dictyostelium discoideum (9)

Repository

ENA (5556)
biostudies-arrayexpress (3936)
geo (513)
pride (452)
MetaboLights (171)
MassIVE (97)
EGA (73)
iProX (46)
jPOST (18)
GPMDB (14)
BioModels (13)
dbGaP (8)
EVA (7)
FAIRDOMHub (7)
PAXDB (7)
PeptideAtlas (5)
GNPS (2)
ExpressionAtlas (1)
Cell Collective (1)
LINCS (1)

Tissue

Cell culture (92)
Brain (28)
Embryo (27)
Whole body (27)
Plant cell (21)
Embryonic stem cell (17)
Leaf (14)
Forebrain and midbrain (1)
Temporal lobe (1)
Diencephalon (1)
Diencephalon and midbrain (1)
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Brain fragment (1)
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Hindbrain fragment (1)
Hindbrain without cerebellum (1)
Stomach (1)
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Hippocampus (1)
Cerebellum (1)
Female Reproductive System (1)

Disease

Normal (8)
Parkinson's disease (5)
Acute myeloid leukemia (3)
Malaria (3)
Cerebral degeneration (1)
Retinal degeneration (1)
Huntington's disease (1)
Ocular albinism (1)
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MAS (1)
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Specific-pathogen free (SPF) (1)
Low-stage neuroblastoma (1)
Post-stasis (1)
Papillary Carcinoma (1)
Blumeria graminis hordei (powdery mildew) inoculation (1)
Chondroblastoma (1)
Squamous cell carcinoma has accession C0007137 in DiseaseStateDatabase NCI_Thesaurus (1)
Infiltrating ductal carcinoma (1)
Xenografts with H1299 cell line (1)
Kaposi's sarcoma (1)
AIDS-KS, HIV+, nodular (late) stage (1)
Basal cell carcinoma, Gorlin-Goltz syndrome (1)
Mock infected (1)
Colon carcinoma (1)

Technology Type

Mass Spectrometry (452)
Shotgun proteomics (213)
Mass spectrometry (133)
Bottom-up proteomics (127)
Data-dependent acquisition (60)
Affinity purification coupled with mass spectrometry proteomics (59)
Data-independent acquisition (36)
Gel-based experiment (33)
Mass spectrometry assay (26)
Chemical cross-linking coupled with mass spectrometry proteomics (16)
NMR spectroscopy (13)
SWATH MS (12)
SRM/MRM (8)
DiaPASEF (7)
Top-down proteomics (7)
HDMSE (5)
Illumina HiSeq 2000 (3)
All-ion fragmentation (3)
Affinity proteomics (2)
Human Cardio Metabochip (1)
ILLUMINA, NextSeq 500 (1)
Illumina HiSeq 2500, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2500 (1)
ILLUMINA, Illumina HiSeq 2500, Illumina HiSeq 2000 (1)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina HiSeq 2500 (1)
Illumina Genome Analyzer II (1)
Fluorescence intensity (1)
KINOMEscan (1)
NMR spectroscopy assay (1)

Instrument Platform

Illumina NovaSeq 6000 (94)
Illumina HiSeq 2000 (53)
Illumina HiSeq 2500 (48)
Illumina HiSeq 4000 (46)
NextSeq 500 (44)
NextSeq 550 (10)
Spectronic Helios Alpha UV-Vis spectrophotometer (7)
Illumina NovaSeq X (7)
Illumina MiSeq (7)
N/A (6)
Affymetrix GeneChip Scanner 3000 7G (5)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (4)
10X Genomics reagent kit (4)
Ultracentrifuge (4)
NanoDrop (4)
Chemostat (3)
Bioanalyser (3)
Variable Atmosphere Incubator (3)
NextSeq 2000 (3)
Illumina HiSeq 1000 (3)
Illumina HiSeq 3000 (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)
Single cells were captured using the 10x Genomics Chromium Controller. (2)
10X Chromium Nuclei Isolation Kit (2)
Chromium 10x (2)
10X Chromium Controller (2)
AB SOLiD 4 System (2)
ScanArray 5000 [PerkinElmer] (2)
Jencons Millennium CO2 Incubator (2)
GeneQuant (2)

Publication Date

2013 (661)
2010 (642)
2011 (479)
2015 (451)
2012 (433)
2014 (379)
2025 (231)
2026 (213)
2008 (206)
2024 (188)
2009 (176)
2016 (172)
2023 (164)
2022 (154)
2021 (145)
2020 (116)
2007 (98)
2017 (93)
2019 (92)
2018 (85)
2005 (50)
2006 (30)
2004 (8)
2003 (4)
2002 (1)

UNIPROT ID/AC

A0A0M4JB57_TOBAC (3)
A0A0M4JJI5_TOBAC (3)
A0A0M4JNG5_TOBAC (3)
A0A0M4JST5_TOBAC (3)
A0A0M5KC92_TOBAC (3)
A0A140G1P7_TOBAC (3)
A0A140G1S2_TOBAC (3)
A0A1S3X5A3_TOBAC (3)
A0A1S3XBM4_TOBAC (3)
A0A1S3XCV6_TOBAC (3)
A0A1S3XE25_TOBAC (3)
A0A1S3XHC2_TOBAC (3)
A0A1S3XU47_TOBAC (3)
A0A1S3XU77_TOBAC (3)
A0A1S3XYI9_TOBAC (3)
A0A1S3Y4V1_TOBAC (3)
Q6GQ63 (1)
P13350 (1)
P70032 (1)
Q9NTU9 (1)
Q3T1B0 (1)
Q9NWT6 (1)
P16157 (1)
Q9Y2N7 (1)
Q99814 (1)
Q16665 (1)
Q8QGV2 (1)
P23437 (1)
P50756 (1)
P35567 (1)

ENSEMBL ID

ENSG00000147251 (1)
ENSG00000170477 (1)
ENSG00000204131 (1)
ENSG00000229353 (1)
ENSG00000247315 (1)
ENSMUSG00000021039 (1)
ENSMUSG00000027651 (1)
ENSMUSP00000141097 (1)

CHEBI ID

CHEBI:15428 (52)
CHEBI:16335 (46)
CHEBI:15741 (45)
CHEBI:30769 (45)
CHEBI:25017 (40)
CHEBI:27266 (40)
CHEBI:18012 (40)
CHEBI:30915 (40)
CHEBI:16704 (39)
CHEBI:25094 (38)
CHEBI:18186 (37)
CHEBI:28300 (37)
CHEBI:28044 (37)
CHEBI:16449 (37)
CHEBI:6650 (36)
CHEBI:17368 (36)
CHEBI:16708 (35)
CHEBI:26271 (34)
CHEBI:24898 (34)
CHEBI:17822 (33)
CHEBI:16811 (33)
CHEBI:15354 (33)
CHEBI:17596 (33)
CHEBI:16919 (32)
CHEBI:27897 (32)
CHEBI:16865 (31)
CHEBI:17895 (31)
CHEBI:18237 (30)
CHEBI:17568 (30)
CHEBI:15379 (1)

Metabolite Name

Adenosine (27)
Inosine (27)
Adenine (26)
L-Tyrosine (26)
Hypoxanthine (25)
L-Tryptophan (24)
Taurine (23)
Creatine (23)
Choline (22)
L-Glutamine (22)
Guanosine (22)
L-Phenylalanine (22)
Glycine (21)
L-Serine (21)
Uridine (21)
Glycine (20)
Citric acid (20)
Xanthine (20)
Leucine (19)
Uracil (19)
L-Histidine (19)
L-Arginine (18)
Succinic acid (18)
Allantoin (18)
Guanine (18)
Myristic acid (18)
L-Aspartic acid (17)
ADP (17)
Stearic acid (17)
Uric acid (17)

First Public Date

2014 (886)
2025 (526)
2024 (507)
2023 (466)
2021 (403)
2019 (397)
2026 (390)
2020 (370)
2022 (362)
2017 (306)
2013 (272)
2018 (265)
2015 (202)
2016 (194)
2012 (5)
2010 (3)
2011 (2)

Modelling Approach

Ordinary differential equation model (6)
Cellular potts model (3)
Logical model (3)
Constraint-based model (1)

Lab affiliation

Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, 55128 Mainz, Germany (7)
Department of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA (6)
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (5)
Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee (5)
Department of Cell & Developmental Biology, University of California, San Diego, La Jolla, CA (4)
Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil (4)
School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, CA, USA (4)
Department of Cell & Developmental Biology, University of California, San Diego, CA 92093, USA. (3)
Department of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA (3)
Executive Science Officer, BioFrontiers InstituteDistinguished ProfessorProfessor, Howard Hughes Medical Institute MOLECULAR CELLULAR AND DEVELOPMENTAL BIOLOGY CU DENVER SCHOOL OF MEDICINE (3)
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium (3)
State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China. (3)
Structural Biology & Developmental Neurobiology Director, St. Jude Proteomics Facility St. Jude Children's Research Hospital 262 Danny Thomas Place, Memphis, TN 38105 (3)
Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA. (2)
Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania (2)
Centre for Functional Ecology, University of Coimbra (2)
Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada; Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada; The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada (2)
Department of Cell and Developmental Biology, Neuroscience Graduate Program, Department of Neurology University of Michigan Medical School, Ann Arbor, MI 48109-2200 (2)
Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA (2)
Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA. (2)
Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria (2)
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands (2)
Department of Molecular, Cellular and Developmental Biology. Yale University, 260 Whitney Ave, New Haven, CT. 06520, USA (2)
Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands (2)
Group Leader Cell&Developmental Biology John Innes Centre Norwich, UK (2)
Head, Chair Plant Biotechnology Faculty of Biology University of Freiburg Schaenzlestrasse 1 D-79104 Freiburg Germany (2)
Institute for Systems Biology (2)
Institute of Genetics & Developmental Biology, Chinese Academy of Sciences (2)
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (2)
Institute of Molecular Biology Ackermannweg 4 55128 Mainz (2)

IsPrivate

False (13)

Model Flag

Non Kinetic (3)

Classification

protozoa (51)
fungi (16)
bacteria (9)
helminths (6)
viruses (2)

Modification

N6 (2)
2x(15)N labeled L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (2071)
RNA-seq of coding RNA (533)
ChIP-seq (395)
ChIP-chip by tiling array (291)
Unknown experiment type (118)
RNA-seq of non coding RNA (111)
Comparative genomic hybridization by array (68)
RNA-seq of coding RNA from single cells (63)
Other (47)
Transcription profiling by tiling array (42)
Methylation profiling by array (39)
Transcription profiling by SAGE (16)
Methylation profiling by high throughput sequencing (15)
DNA-seq (14)
ChIP-chip by array (10)
High-throughput sequencing (9)
Genotyping by array (9)
Cell line - High-throughput sequencing (7)
ScATAC-seq (7)
Single nucleus RNA sequencing (7)
MicroRNA profiling by array (7)
RNA-seq of total RNA (7)
Plant - High-throughput sequencing (5)
Bisulfite-seq (5)
Animal - High-throughput sequencing (4)
RNAi profiling by array (4)
Human - Single-cell sequencing (3)
Transcription profiling by RT-PCR (3)
Genotyping by high throughput sequencing (3)
Baseline (2)

Release Date

2021 (6550)
2022 (5562)
2020 (4869)
2023 (4743)
2025 (4590)
2024 (3988)
2019 (3639)
2018 (3581)
2015 (3524)
2016 (3341)
2014 (3288)
2017 (3258)
2013 (2715)
2012 (2340)
2011 (2172)
2010 (2154)
2009 (1490)
2008 (1397)
2007 (926)
2006 (588)
2026 (579)
2005 (415)
2004 (268)
2003 (203)
2002 (145)
2001 (120)
2000 (102)
1999 (91)
1998 (79)
1997 (28)

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Growth control of the eukaryote cell: a systems biology study in yeast

Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each function...

2012-04-19 | MTBLS8 | MetaboLights

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning a...

2018-07-31 | MTBLS492 | MetaboLights

The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis

Drastic alteration in macronutrients causes large changes in gene expression in the photosynthetic unicellular alga Chlamydomonas reinhardtii. Preliminary data suggested that cells follow a biphasic response to this change hinging on the initiation of lipid accumulation, and we hypothesized that ...

2015-06-29 | MTBLS208 | MetaboLights

Cell-based and multi-omics profiling reveal dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei

Mitochondrial metabolic remodeling is a hallmark of the Trypanosoma brucei digenetic life cycle since the insect stage utilizes the cost-effective oxidative phosphorylation to generate ATP, while bloodstream cells switch to less energetically efficient aerobic glycolysis. Due to difficulties in a...

2020-08-20 | MTBLS1390 | MetaboLights

Human Developmental Biology Resource (HDBR) expression resource-RNAseq

The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840, this submission) and HDBR expression resource- SNP...

ORGANISM(S): Homo sapiens

2016-10-12 | E-MTAB-4840 | biostudies-arrayexpress

Human Developmental Biology Resource (HDBR) expression resource-RNAseq

PRJEB14594 | ENA

Genotyping by array: Human Developmental Biology Resource (HDBR) expression resource of prenatal human brain development-SNP data

The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840) and HDBR expression resource- SNP data (E-MTAB-484...

ORGANISM(S): Homo sapiens

2016-10-12 | E-MTAB-4843 | biostudies-arrayexpress

The Childhood Solid Tumor Network: A new resource for the developmental biology and oncology research communities.

Not available

S-EPMC4600003 | biostudies-literature

Budgett's frog (Lepidobatrachus laevis): A new amphibian embryo for developmental biology.

Not available

S-EPMC4670266 | biostudies-literature

Illuminating developmental biology through photochemistry.

Not available

S-EPMC5511696 | biostudies-literature