Co-purification

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Unknown (1026)
Transcriptomics (928)
Genomics (481)
Proteomics (321)
Other (12)
Metabolomics (12)
Methylation profiling (1)

Organisms

Homo sapiens (383)
Mus musculus (260)
Drosophila melanogaster (121)
Saccharomyces cerevisiae (38)
Danio rerio (35)
Arabidopsis thaliana (34)
Rattus norvegicus (33)
Candida albicans (19)
Zea mays (15)
Escherichia coli (7)
Gallus gallus (7)
Escherichia coli K-12 (7)
Bos taurus (6)
Caenorhabditis elegans (6)
Sus scrofa (6)
Oryza sativa (5)
Pseudomonas putida (5)
synthetic construct (4)
Solanum tuberosum (4)
Schizosaccharomyces pombe (4)
Clostridium botulinum (3)
Apis mellifera (3)
Bacillus subtilis (3)
Mycobacterium tuberculosis (3)
Ovis aries (3)
Oryza sativa Japonica Group (3)
Lathyrus sativus (2)
Agrobacterium tumefaciens (2)
environmental samples (2)
Bifidobacterium breve UCC2003 (2)

Organisms

Homo sapiens (76)
Mus musculus (51)
Saccharomyces cerevisiae (10)
Arabidopsis thaliana (9)
Escherichia coli K-12 (8)
Drosophila melanogaster (8)
Nitratidesulfovibrio vulgaris str. Hildenborough (6)
Staphylococcus aureus (4)
Zea mays (4)
Escherichia coli (3)
Danio rerio (3)
Rattus norvegicus (3)
Synechocystis sp. PCC 6803 (2)
African swine fever virus (2)
Schizosaccharomyces pombe (2)
Vitis vinifera (2)
Pseudomonas aeruginosa (2)
Caenorhabditis elegans (2)
Paracidovorax avenae RS-1 (1)
Amphidinium carterae (1)
Nicotiana attenuata (1)
Thujopsis dolabrata var. hondae (1)
Trypanosoma brucei (1)
Porcine epidemic diarrhea virus (1)
Escherichia coli BW25113 (1)
Nostoc sp. PCC 7120 = FACHB-418 (1)
insect metagenome (1)
Actinobacillus pleuropneumoniae (1)
Actinidia chinensis (1)
Klebsiella ornithinolytica (1)

Repository

biostudies-arrayexpress (1059)
ENA (274)
pride (244)
geo (85)
MassIVE (41)
jPOST (29)
MetaboLights (9)
iProX (6)
EGA (4)
GNPS (3)
NODE (3)
EVA (2)

Tissue

Cell culture (65)
Epithelial cell (18)
Cell suspension culture (15)
Permanent cell line cell (14)
Blood (7)
Blood cell (6)
Fibroblast (6)
Kidney (6)
Plant cell (6)
T cell (6)
HEK-293T cell (5)
Whole body (5)
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Blood plasma (3)
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Umbilical cord (2)
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Egg (2)
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Heart (2)
Hepatocyte (2)
Leaf (2)
Liver (2)
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Retina (2)
Root (2)
Spleen (2)

Disease

Disease free (9)
Normal (5)
Breast cancer (4)
Plasmodium falciparum malaria (4)
Alzheimer's disease (2)
Colon cancer (2)
Malaria (2)
Trypanosomiasis (2)
Type 2 diabetes mellitus (2)
HPV positive (1)
Perilobar nephrogenic rest (1)
Microscopic Polyangiitis (1)
Autoimmune disorder (1)
Infected with IBDV strain F52/70 (1)
Scrapie infected (1)
None- acute control (1)
None- Acute Control (1)
Idiopathic dilated cardiomyopathy (1)
Glioblastoma (1)
Prostate cancer (1)
Prostate carcinoma (1)
Wilms tumour (1)
Acute leukemia (1)
Acute myeloid leukemia (1)
Adult respiratory distress syndrome (1)
Ankylosis (1)
COVID-19 (1)
Chronic myeloid leukemia (1)
Ciliopathy (1)
Cystic fibrosis (1)

Technology Type

Mass Spectrometry (244)
Affinity purification coupled with mass spectrometry proteomics (116)
Shotgun proteomics (87)
Bottom-up proteomics (36)
Gel-based experiment (24)
Data-dependent acquisition (23)
Data-independent acquisition (11)
Mass spectrometry (9)
Chemical cross-linking coupled with mass spectrometry proteomics (5)
SWATH MS (5)
Top-down proteomics (5)
HDMSE (2)
454 GS FLX Titanium, Illumina HiSeq 2000 (1)
Affinity proteomics (1)
MSE (1)
Mass spectrometry imaging (1)
Metaproteomics (1)
SRM/MRM (1)

Instrument Platform

Illumina NovaSeq 6000 (71)
NextSeq 500 (23)
Illumina HiSeq 4000 (18)
Illumina HiSeq 2500 (15)
Illumina HiSeq 2000 (14)
Illumina MiSeq (9)
NextSeq 2000 (8)
Illumina NovaSeq X (7)
NextSeq 550 (7)
Axon GenePix 4000B scanning hardware (5)
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)
Agilent High resolution C scanner (2)
ScanArray Lite [PerkinElmer] (2)
GenePix Personal 4100A [Axon Instruments] (2)
NextSeq 1000 (2)
NA (2)
Illumina HiSeq X (2)
N/A (2)
DNBSEQ-T7 (2)
Illumina HiSeq 1500 (2)
Illumina HiSeq 3000 (2)
Gentle MACS; BD FACS Aria III (1)
ICELL8 MultiSample NanoDispenser (1)
Qiagen RNEasy Mini ki (1)
BD FACSAriaIIu cell sorter (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
Poly-T oligo-attached magnetic beads (1)

Publication Date

2013 (190)
2010 (126)
2025 (113)
2014 (113)
2026 (106)
2012 (98)
2015 (84)
2011 (79)
2022 (61)
2016 (60)
2024 (57)
2008 (56)
2021 (50)
2023 (49)
2009 (46)
2020 (40)
2019 (35)
2017 (30)
2018 (27)
2007 (26)
2005 (12)
2006 (11)
2004 (4)
2003 (4)

CHEBI ID

CHEBI:17754 (4)
CHEBI:16000 (4)
CHEBI:16865 (4)
CHEBI:15428 (4)
CHEBI:16335 (4)
CHEBI:17992 (3)
CHEBI:18257 (3)
CHEBI:16958 (3)
CHEBI:17148 (3)
CHEBI:17115 (3)
CHEBI:15741 (3)
CHEBI:18019 (3)
CHEBI:33508 (3)
CHEBI:18012 (3)
CHEBI:16414 (3)
CHEBI:15603 (3)
CHEBI:17596 (3)
CHEBI:26078 (3)
CHEBI:15440 (2)
CHEBI:27693 (2)
CHEBI:43619 (2)
CHEBI:18186 (2)
CHEBI:30794 (2)
CHEBI:15699 (2)
CHEBI:16551 (2)
CHEBI:4167 (2)
CHEBI:17561 (2)
CHEBI:422 (2)
CHEBI:16704 (2)
CHEBI:16857 (2)

Metabolite Name

Ethanolamine (3)
Glycine (3)
Ornithine (3)
Adenosine (3)
Phosphoric acid (2)
Glycerol (2)
Glycerol (2)
Mannitol (2)
Nicotinic acid (2)
Putrescine (2)
Cholesterol (2)
Cis-Aconitic acid (2)
Pantothenic acid (2)
L-Lysine (2)
Succinic acid (2)
Fumaric acid (2)
Glyceric acid (2)
L-Tryptophan (2)
L-Glutamine (2)
L-Serine (2)
Uridine (2)
Sucrose (2)
Glycerophosphocholine (2)
L-Valine (2)
L-Leucine (2)
L-Tyrosine (2)
L-Phenylalanine (2)
Inosine (2)
Glycerol-2-phosphoric acid (1)
1-Pyrroline-3-hydroxy-5-carboxylic acid (1)

First Public Date

2014 (47)
2025 (37)
2024 (34)
2023 (28)
2022 (20)
2026 (19)
2021 (17)
2018 (15)
2019 (12)
2013 (12)
2017 (11)
2016 (9)
2015 (7)
2020 (6)

Classification

bacteria (23)
viruses (3)
protozoa (2)

Modification

15.994915 (1)
57.021464 (1)
6.020129 (1)
79.966331 (1)

Study type

Transcription profiling by array (508)
ChIP-seq (160)
RNA-seq of coding RNA (153)
Other (26)
RNA-seq of coding RNA from single cells (24)
ChIP-chip by tiling array (22)
Comparative genomic hybridization by array (20)
RNA-seq of non coding RNA (19)
Unknown experiment type (18)
ChIP-chip by array (17)
RNA-seq of total RNA (13)
DNA-seq (12)
Transcription profiling by tiling array (8)
Single nucleus RNA sequencing (6)
Methylation profiling by array (6)
Methylation profiling by high throughput sequencing (6)
Transcription profiling by SAGE (5)
Genotyping by array (4)
Transcription profiling by RT-PCR (4)
MicroRNA profiling by high throughput sequencing (3)
Human - High-throughput sequencing (2)
Cell line - High-throughput sequencing (2)
ATAC-seq (2)
RIP-seq (2)
Ribo-seq (2)
MicroRNA profiling by array (2)
Two-color microarray (1)
MeDIP-seq (1)
Animal - One-color microarray (1)
One-color microarray (1)

Release Date

2013 (224)
2025 (165)
2010 (148)
2014 (147)
2012 (127)
2015 (114)
2011 (109)
2022 (108)
2016 (104)
2021 (97)
2024 (93)
2023 (91)
2026 (77)
2019 (74)
2020 (73)
2008 (72)
2017 (67)
2018 (54)
2009 (54)
2007 (33)
2006 (22)
2005 (15)
2004 (6)
2003 (3)
2001 (3)
2002 (2)
2000 (2)
1997 (1)

Lab affiliation

Protein Biogenesis Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT (4)
Molecular Genetics, TU Kaiserslautern (3)
Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA. (2)
Fundação Oswaldo Cruz - Instituto Carlos Chagas (2)
Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany (2)
Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany. (2)
UCSF (2)
University of Toronto (2)
(1) Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; (2) VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium. (1)
1,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China 2,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China (1)
1. Center for Medical Biotechnology, VIB, Ghent, Belgium. 2. Department for Biomolecular Medicine, Ghent University, Ghent, Belgium 3. VIB Proteomics Core, VIB, Ghent, Belgium (1)
1. Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; 2. Centre for Analytical Sciences Amsterdam (CASA), The Netherlands (1)
1. Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 2. Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan (1)
1. Laboratorio de Enfermedades Parasitarias, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela 2. Department of Biomedical Sciences, School of Medicine, University of Minnesota Duluth. 1035 University Drive, Duluth, MN, 55812 USA (1)
AG Willmitzer, Max Planck Institute of Molecular Plants Physiology, Potsdam-Golm, Germany (1)
Agrochemistry and Biochemistry Department. University of Alicante (1)
Aix-Marseille University, INSERM, TAGC, UMR_S1090, Marseille, France (1)
Anonymity for double-blind review (1)
Assistant Professor, Gene Expression & Regulation Program, Wistar Institute Cancer Center, Philadelphia PA, USA (1)
Associate Member Developmental Neurobiology St. Jude Children's Research Hospital (1)
Associate Professor, Department of Neurology, UNC-Chapel Hill (1)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (1)
Beijing University of Agriculture, Beijing, China (1)
Beijing, You An Men Wai Xi Tou Tiao No.10 Capital Medical University, Beijing Laboratory of Oral Health (1)
Beijing, You An Men Wai Xi Tou Tiao No.10, Capital Medical University, Beijing Laboratory of Oral Health (1)
Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia (1)
Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3052, Australia (1)
Biomolecular Mass Spectrometry and Proteomics (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands and Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands (1)

2785 Results

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