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Unknown (4480)
Transcriptomics (1164)
Genomics (391)
Proteomics (324)
Metabolomics (107)
Other (18)
Methylation profiling (11)
Genomic (8)
Models (3)
Multiomics (1)

Organisms

Homo sapiens (497)
Mus musculus (480)
Drosophila melanogaster (79)
Rattus norvegicus (62)
Saccharomyces cerevisiae (45)
Arabidopsis thaliana (22)
Apis mellifera (14)
Sus scrofa (13)
Caenorhabditis elegans (13)
Danio rerio (12)
Eohaustorius estuarius (11)
Bombyx mori (9)
Aplysia californica (6)
Gallus gallus (6)
Tetrahymena thermophila (4)
Myxococcus xanthus (4)
Spodoptera frugiperda (4)
Schistosoma mansoni (4)
Solenopsis invicta (4)
Saccharomyces cerevisiae Sigma1278b (4)
Oryza sativa (3)
Nicotiana tabacum (3)
Anopheles gambiae (3)
Macaca mulatta (3)
Chlamydomonas reinhardtii (3)
Sphyracephala beccarii (2)
Chlamydia trachomatis (2)
Haemophilus influenzae (2)
Drosophila simulans (2)
Zea mays (2)

Organisms

Homo sapiens (79)
Mus musculus (38)
Saccharomyces cerevisiae (16)
Drosophila melanogaster (10)
Caenorhabditis elegans (5)
Arabidopsis thaliana (4)
Pleurocybella porrigens (3)
hypersaline lake metagenome (2)
Escherichia coli str. K-12 substr. MG1655 (2)
Camellia sinensis (2)
Bombyx mori (2)
Plasmodium falciparum (2)
Gallus gallus (2)
Paraphaeosphaeria (1)
Pyronema omphalodes (1)
Plasmodium yoelii yoelii 17XNL (1)
Paxillus involutus (1)
Phycomyces blakesleeanus (1)
Plasmodium falciparum 3D7 (1)
Cryptococcus neoformans H99 (1)
Saccharomyces cerevisiae SK1 (1)
Chlamydomonas reinhardtii (1)
Saccharomyces cerevisiae Sigma1278b (1)
Nothobranchius furzeri (1)
Chlorocebus sabaeus (1)
Ovis aries (1)
Escherichia coli K-12 (1)
Plasmodium berghei (1)
Rattus norvegicus (1)

Repository

biostudies-arrayexpress (1183)
ENA (230)
pride (178)
geo (161)
MetaboLights (106)
MassIVE (69)
jPOST (33)
PAXDB (20)
PeptideAtlas (14)
EGA (12)
dbGaP (8)
iProX (7)
PanoramaPublic (3)
BioModels (2)
ExpressionAtlas (1)
Cell Collective (1)
GPMDB (1)

Tissue

Cell culture (43)
Brain (23)
Others (14)
Blood (9)
Blood cell (7)
Endothelial cell (6)
Epithelial cell (6)
Embryonic stem cell (5)
Bone marrow (4)
Whole body (4)
Embryo (3)
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Heart (3)
Lung (3)
Plant cell (3)
Primary cell (3)
Seedling (3)
T cell (3)
Urine (3)
B cell (2)
Blood plasma (2)
Blood serum (2)
Cell suspension culture (2)
Colon (2)
Early embryonic cell (2)
Endothelial cell of umbilical vein (2)
Jump-In-T-REx HEK293 cell (2)
Leaf (2)
Liver (2)
Macrophage (2)

Disease

Parkinson's disease (8)
Lewy body dementia (4)
Normal (3)
Acute leukemia (3)
Melanoma (3)
Brain cancer (2)
Colon cancer (2)
Lung carcinoma (2)
Plasmodium falciparum malaria (2)
Uninfected 11dpi (1)
Neurologically healthy control (1)
No disease (1)
Not Available (1)
Acute myeloid leukemia (1)
Breast cancer (1)
Childhood extraosseous osteosarcoma (1)
Cholangiocarcinoma (1)
Chronic bronchitis (1)
Chronic kidney disease (1)
Collagen disease (1)
Colorectal cancer (1)
Cutaneous leishmaniasis (1)
Cystic fibrosis (1)
Embryonal rhabdomyosarcoma (1)
Encephalopathy (1)
Fibrosarcoma (1)
Head and neck cancer (1)
Hermansky-Pudlak syndrome 2 (1)
Ischemic stroke (1)
Kabuki syndrome (1)

Technology Type

Mass Spectrometry (178)
Shotgun proteomics (88)
Mass spectrometry (57)
Mass spectrometry assay (41)
Bottom-up proteomics (38)
Affinity purification coupled with mass spectrometry proteomics (25)
Gel-based experiment (20)
Data-independent acquisition (16)
Data-dependent acquisition (13)
NMR spectroscopy (7)
SWATH MS (7)
Chemical cross-linking coupled with mass spectrometry proteomics (3)
Top-down proteomics (3)
DiaPASEF (2)
Illumina Genome Analyzer IIx (1)
NMR spectroscopy assay (1)
Mass spectrometry imaging (1)

Instrument Platform

Illumina NovaSeq 6000 (74)
NextSeq 500 (32)
Illumina HiSeq 4000 (29)
Illumina HiSeq 2500 (17)
NextSeq 550 (15)
Illumina NovaSeq X (14)
Illumina HiSeq 2000 (10)
NextSeq 2000 (5)
Illumina MiSeq (4)
None (3)
Illumina Genome Analyzer IIx (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)
The Agilent scanner G2565BA (2)
Agilent�s Microarray Hybridization Oven (2)
NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies) (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)
NanoDrop 2000 Spectrophotometer, Agilent 2100 Bioanalyzer (1)
Scanpy (hash 98de5d1a) (1)
Chromium Next GEM Single Cell 5' Reagent Kits (10x Genomics) (1)
10xGenomics Chromium 3'v3 (1)
CryoStor® CS10 Freezing Medium (Cat. No. 100-1061; StemCell Technologies) (1)
10x Genomics Chromium Controller, PCR thermocycler, Agilent 2100 Bioanalyzer with High Sensitivity DNA chip (for quality control) (1)
Water bath (for enzymatic dissociation), cell strainer (70-μm), benchtop centrifuge, automated cell counter/hemocytometer, biological safety cabinet (1)
Sterile surgical instrument set (scalpels, tissue forceps, dissection scissors), animal operating table, biological safety cabinet (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
NaN (1)

Publication Date

2015 (163)
2014 (161)
2025 (141)
2013 (139)
2010 (133)
2012 (128)
2026 (118)
2011 (108)
2024 (93)
2023 (91)
2016 (91)
2020 (61)
2022 (58)
2021 (52)
2018 (44)
2009 (42)
2019 (40)
2008 (36)
2017 (30)
2007 (17)
2006 (11)
2005 (7)
2004 (5)

UNIPROT ID/AC

1433S_HUMAN (19)
A1AG1_HUMAN (19)
A1AG2_HUMAN (19)
A1AT_HUMAN (19)
A1BG_HUMAN (19)
A2AP_HUMAN (19)
A2GL_HUMAN (19)
A2MG_HUMAN (19)
AACT_HUMAN (19)
ACTG_HUMAN (19)
ACTS_HUMAN (19)
ADIPO_HUMAN (19)
AFAM_HUMAN (19)
ALBU_HUMAN (19)
AMBP_HUMAN (19)
AMPN_HUMAN (19)
ANGT_HUMAN (19)
ANT3_HUMAN (19)
APMAP_HUMAN (19)
APOA1_HUMAN (19)
APOA2_HUMAN (19)
APOA4_HUMAN (19)
APOB_HUMAN (19)
APOC1_HUMAN (19)
APOC2_HUMAN (19)
APOC3_HUMAN (19)
APOD_HUMAN (19)
APOE_HUMAN (19)
P47113 (2)
P38987 (2)

ENSEMBL ID

ENSG00000170477 (14)
ENSG00000247315 (3)
ENSG00000147251 (1)

CHEBI ID

CHEBI:30769 (20)
CHEBI:28044 (17)
CHEBI:18237 (16)
CHEBI:18186 (16)
CHEBI:15891 (16)
CHEBI:15428 (15)
CHEBI:15741 (15)
CHEBI:27266 (15)
CHEBI:17750 (15)
CHEBI:15354 (15)
CHEBI:17368 (15)
CHEBI:17822 (14)
CHEBI:16811 (14)
CHEBI:16704 (14)
CHEBI:18012 (14)
CHEBI:16737 (14)
CHEBI:26986 (13)
CHEBI:25017 (13)
CHEBI:16335 (13)
CHEBI:32816 (13)
CHEBI:27897 (13)
CHEBI:17596 (13)
CHEBI:25094 (12)
CHEBI:27570 (12)
CHEBI:28300 (12)
CHEBI:18257 (12)
CHEBI:24898 (12)
CHEBI:30915 (12)
CHEBI:17552 (8)
CHEBI:15996 (2)

Metabolite Name

Inosine (25)
Adenine (22)
Adenosine (20)
Creatinine (20)
Guanosine (19)
Creatine (19)
Hypoxanthine (19)
Betaine (18)
Taurine (17)
Ornithine (16)
Tyrosine (16)
Phenylalanine (16)
Uridine (16)
L-Tyrosine (16)
Methionine (15)
Tryptophan (15)
Choline (14)
Xanthosine (14)
Lysine (14)
Glutamine (14)
Glycerophosphocholine (14)
Histidine (13)
Leucine (13)
L-Threonine (13)
L-Histidine (13)
Guanine (13)
Sucrose (13)
L-Phenylalanine (13)
Glycine (12)
Citrulline (12)

First Public Date

2024 (39)
2025 (31)
2026 (26)
2014 (22)
2023 (15)
2022 (13)
2013 (13)
2019 (12)
2015 (12)
2021 (11)
2020 (11)
2018 (11)
2017 (11)
2016 (3)

Modelling Approach

Ordinary differential equation model (2)

Lab affiliation

IMSB, ETH Zurich (4)
Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany (4)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (4)
Huazhong University of Science and Technology (3)
Molecular Genetics, RPTU Kaiserslautern (3)
UMR 7367 CNRS-UL IMoPA Biopôle de l'Université de Lorraine Campus Brabois-Santé 9 avenue de la forêt de Haye 54505 Vandoeuvre-les-Nancy FRANCE (3)
College of Plant Protection, Northwest A&F University (2)
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)
Helmholtz Munich (2)
Laboratory for Cell Biology and Signalling, Division of Molecular Biology, Ruder Boskovic Institute, Zagreb, Croatia (2)
Molecular Genetics, RPTU Kaiserslautern, Germany (2)
School of Biomedical and Healthcare Sciences; Plymouth University (UK) (2)
1 Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin 2 Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France 3 Laboratoire d’excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France 4 Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France (1)
1 Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin 2 Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France 3 Laboratoire d’excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France 4 Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France (1)
1. Institut de Recherche en Immunologie et Cancérologie (IRIC), Université de Montréal, Montréal, Québec, Canada. 2. Département de Biochimie et Biologie Moléculaire, Université de Montréal, Montréal, Québec, Canada. 3. Département de Chimie, Université de Montréal, Montréal, Québec, Canada (1)
Associate Professor Department of Physiology Medical College of Wisconsin (1)
Beijing proteome research center (1)
BioOrganic Mass Spectrometry laboratory (LSMBO) Institut Plurisciplinaire Hubert Curien University of Strasbourg. France (1)
Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA. (1)
Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA. (1)
Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA (1)
Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), Copenhagen, Denmark (1)
Biotechnology Research Center, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China (1)
Bristol Medical School, University of Bristol (1)
Cancer Research Center of Toulouse (CRCT) 2 Avenue Hubert Curien 31037 Toulouse (1)
Cancer Research UK Cambridge Institute University of Cambridge Li Ka Shing Centre Cambridge CB2 0RE United Kingdom (1)
Cell and Chemical Biology Leiden University Medical Center (1)
Cell and Chemical Biology Leiden University Medical Center Leiden The Netherlands (1)
Cell and Chemical Biology Leiden University Medical Center The Netherlands (1)
Cellular and Molecular Pathology, UCSF (1)

IsPrivate

False (2)

Classification

protozoa (5)
bacteria (3)
fungi (2)

Modification

15.994915 (1)
2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)
57.021464 (1)

Study type

Transcription profiling by array (630)
RNA-seq of coding RNA (143)
ChIP-seq (96)
RNA-seq of coding RNA from single cells (82)
Methylation profiling by array (40)
Methylation profiling by high throughput sequencing (29)
ChIP-chip by tiling array (24)
RNA-seq of non coding RNA (21)
Other (16)
RNA-seq of total RNA (15)
Comparative genomic hybridization by array (13)
Unknown experiment type (12)
ChIP-chip by array (6)
Cell line - High-throughput sequencing (5)
MicroRNA profiling by high throughput sequencing (4)
ATAC-seq (4)
Single nucleus RNA sequencing (4)
High-throughput sequencing (3)
Bisulfite-seq (3)
Transcription profiling by SAGE (2)
Cell line - Single-cell sequencing (2)
Differential (2)
Cell line - One-color microarray (2)
Animal - High-throughput sequencing (2)
Transcription profiling by tiling array (2)
Transcription profiling by RT-PCR (2)
ScATAC-seq (2)
MicroRNA profiling by array (2)
Metabolomic profiling (1)
RNA-seq of non coding RNA from single cells (1)

Release Date

2022 (523)
2023 (491)
2025 (482)
2024 (450)
2021 (441)
2020 (370)
2019 (323)
2015 (293)
2016 (260)
2013 (260)
2014 (259)
2018 (248)
2012 (227)
2017 (198)
2010 (195)
2011 (176)
2026 (99)
2009 (95)
2008 (89)
2007 (58)
2006 (43)
2005 (21)
2004 (16)
2003 (11)
2001 (9)
1999 (9)
2002 (7)
2000 (5)
1998 (4)
1997 (1)

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Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants

Brassicaceae plants have a dual-cell type of chemical defense against herbivory. Here we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body β-glucosidases BG...

2020-02-04 | MTBLS1383 | MetaboLights

The Parkinson's disease protein alpha-synuclein is a direct modulator of Processing-bodies and mRNA stability

Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR,Carr SA, de Jager P, Myers CL, Lindquist S, Greenmyre TJ, Bartel DP, Feany MB, Sunyaev S, Chung CY and Khurana V. Alp...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2022-03-09 | MSV000089026 | MassIVE

RNA-Seq of purified P-bodies from HEK293 cells

To identify RNAs accumulating in P-bodies (cytoslic RNP granules), P-bodies were purified from HEK293 cell extracts using a Flow Activated Particle Sorting (FAPS) method. Sorted P-bodies were compared to the pre-sorted fraction to identify RNA enriched in P-bodies.

ORGANISM(S): Homo sapiens

2017-09-01 | E-MTAB-5477 | biostudies-arrayexpress

P-bodies dynamics of hESCs by unveiling P-bodies properties of hESC and hESC-derived mesodermal cells

PRJNA1033589 | ENA

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

RNA-Seq of purified P-bodies from HEK293 cells

PRJEB19388 | ENA

RNA sequestration in P-bodies sustains myeloid leukemia [P-body-seq]

PRJNA932348 | ENA

RNA sequestration in P-bodies sustains myeloid leukaemia

PRJNA1084006 | ENA

RNA sequestration in P-bodies sustains myeloid leukaemia

PRJNA931996 | ENA

Selective RNA sequestration in P-bodies regulates cell identity

Post-transcriptional regulation is pivotal in guiding the gene expression programs that instruct cell fate decisions. Recent studies emphasize the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of...

ORGANISM(S): Mus musculus (Mouse)

2025-05-07 | PXD058827 | Pride

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OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
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NODE

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6509 Results

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