Encyclopedia - OmicsDI

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Unknown (11282)
Genomics (4862)
Proteomics (876)
Transcriptomics (603)
Metabolomics (142)
Other (12)
Methylation profiling (11)
Genomic (2)
Models (1)

Organisms

Homo sapiens (341)
Mus musculus (238)
Rattus norvegicus (64)
Bos taurus (18)
Gallus gallus (18)
Caenorhabditis elegans (14)
Sus scrofa (14)
Danio rerio (10)
Drosophila melanogaster (9)
Ovis aries (8)
Triticum aestivum (6)
Escherichia coli (4)
Bombyx mori (3)
Oryza sativa (3)
Solanum chilense (2)
Gastrodia elata (2)
Drosophila ficusphila (2)
Manihot esculenta (2)
Macaca mulatta (2)
Apis mellifera (2)
Coccinella septempunctata (1)
Rapana venosa (1)
Camellia sinensis (1)
Hevea brasiliensis (1)
human oral metagenome (1)
Bemisia tabaci (1)
Panax ginseng (1)
Panonychus citri (1)
Cricetulus griseus (1)
Oryza sativa Japonica Group (1)

Organisms

Homo sapiens (259)
Mus musculus (199)
Salinibacter ruber (80)
Rattus norvegicus (63)
Rhizobium leguminosarum (31)
Rhizobium esperanzae (17)
Bos taurus (16)
Agrobacterium tumefaciens (15)
Gallus gallus (14)
Methanococcus maripaludis (13)
Sus scrofa (13)
Danio rerio (13)
Paraburkholderia youngii (12)
Bradyrhizobium sp. BTAi1 (12)
Polynucleobacter sphagniphilus (10)
Aurantimicrobium minutum (10)
Stutzerimonas stutzeri RCH2 (9)
Paraburkholderia atlantica (8)
Rhizobium etli (8)
Photorhabdus luminescens (7)
Shewanella amazonensis SB2B (7)
Pedobacter cryoconitis (6)
Photorhabdus temperata (6)
Oncorhynchus mykiss (6)
Nocardia amikacinitolerans (5)
Azotobacter beijerinckii (5)
Paraburkholderia lebeckiae (5)
Rhizobium aethiopicum (5)
Phaeobacter gallaeciensis DSM 26640 (5)
Drosophila melanogaster (5)

Repository

ENA (4748)
pride (703)
geo (570)
biostudies-arrayexpress (160)
MetaboLights (138)
iProX (137)
PeptideAtlas (19)
MassIVE (12)
EGA (8)
GNPS (3)
PAXDB (3)
dbGaP (2)
NODE (2)
ExpressionAtlas (1)
BioModels (1)
GPMDB (1)
jPOST (1)
MetabolomicsWorkbench (1)

Tissue

Cell culture (127)
Brain (46)
Leaf (38)
Whole body (34)
Epithelial cell (31)
Heart (24)
Plant cell (23)
Blood serum (21)
Liver (21)
Blood plasma (19)
Others (18)
Root (17)
Lung (14)
Blood cell (13)
Colon (12)
Macrophage (11)
Skin (10)
Testis (10)
Cell suspension culture (9)
Permanent cell line cell (9)
Kidney (9)
Blood (9)
Bone marrow (8)
Fibroblast (8)
Retina (7)
Stem cell (7)
Spleen (7)
B cell (7)
Pancreas (3)
Cultured cells (1)

Disease

Oral squamous cell carcinoma (2)
Endometrium adenocarcinoma (1)
Gastric tubular adenocarcinoma (1)
Undifferentiated carcinoma (1)
Amelanotic melanoma (1)
Salivary gland squamous cell carcinoma (1)
Endometrial endometrioid adenocarcinoma, variant with squamous differentiation (1)
Ovarian endometrioid adenocarcinoma (1)
Gliosarcoma (1)
B-cell prolymphocytic leukemia (1)
Childhood acute monocytic leukemia (1)
Mucinous gastric adenocarcinoma (1)
Hereditary thyroid gland medullary carcinoma (1)
Extrarenal rhabdoid tumor (1)
Meningioma (1)
Leiomyoma, epithelioid (1)
Primary effusion lymphoma (1)
Cecum adenocarcinoma (1)
Bronchioloalveolar carcinoma (1)
Adenosquamous lung carcinoma (1)
Pancreatic adenosquamous carcinoma (1)
Laryngeal squamous cell carcinoma (1)
Duodenal adenocarcinoma (1)
Adult B acute lymphoblastic leukemia (1)
Uterine leiomyosarcoma (1)
Endometrial stromal sarcoma (1)
Chronic eosinophilic leukemia (1)
Ampulla of Vater adenocarcinoma (1)
Cutaneous melanoma (1)
Colon carcinoma (1)

Technology Type

Mass Spectrometry (704)
Shotgun proteomics (425)
Bottom-up proteomics (120)
Mass spectrometry (97)
Data-independent acquisition (58)
Data-dependent acquisition (49)
SWATH MS (45)
Mass spectrometry assay (39)
Top-down proteomics (20)
Affinity purification coupled with mass spectrometry proteomics (20)
Gel-based experiment (16)
All-ion fragmentation (13)
Mass spectrometry imaging (6)
MSE (5)
SRM/MRM (5)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
NMR spectroscopy (3)
Affinity proteomics (3)
Proteogenomics (2)
HDMSE (2)
Illumina CytoSNP, Illumina HumanOmni2.5, ILLUMINA, Illumina 450k, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000 (1)
ESI (1)
Metaproteomics (1)
Immunopeptidomics (1)
DiaPASEF (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (41)
Liquid Chromatography MS - negative - reverse phase (36)
Liquid Chromatography MS - positive - reverse-phase (25)
Liquid Chromatography MS - negative - reverse-phase (25)
Liquid Chromatography MS - negative - hilic (17)
Liquid Chromatography MS - positive - hilic (16)
LTQ Orbitrap Velos (9)
Illumina HiSeq 2000 (7)
Liquid Chromatography MS - negative (7)
Liquid Chromatography MS - positive (7)
Liquid Chromatography MS - alternating - hilic (7)
TripleTOF 5600 (6)
Illumina NovaSeq 6000 (3)
MS:1000419 (3)
Q Exactive (3)
Axon GenePix4000B (2)
Illumina HiSeq 4000 (2)
TSQ Vantage (Thermo Scientific) (2)
MS:1000044 (2)
MS:1000031 (2)
Orbitrap Fusion (2)
LTQ Orbitrap (2)
Computer (1)
Illumina HiSeq 1500 (1)
7890A GC coupled to a 5975C inert XL MSD, with a 7683 series injector (G2614A) (1)
TripleTOF 5600+ (1)
Instrument (1)
LTQ XL (1)
LTQ Orbitrap Elite (1)
Orbitrap Fusion Lumos (1)

Publication Date

2022 (235)
2021 (199)
2025 (198)
2024 (161)
2026 (160)
2023 (149)
2020 (113)
2019 (86)
2018 (67)
2010 (46)
2014 (43)
2015 (37)
2017 (34)
2013 (34)
2012 (26)
2008 (24)
2016 (23)
2009 (20)
2011 (11)
2006 (8)
2007 (6)
2005 (4)

UNIPROT ID/AC

G1SVB3_RABIT (1)
A0A5F9C4L7_RABIT (1)
G1TKE5_RABIT (1)
G1T4D5_RABIT (1)
G1U8G0_RABIT (1)
G1SSN8_RABIT (1)
G1T4N8_RABIT (1)
G1SMH9_RABIT (1)
G1U2A1_RABIT (1)
G1U3Q6_RABIT (1)
A0A5F9CGP0_RABIT (1)
SAA2_RABIT (1)
G1T2S0_RABIT (1)
G1TDT3_RABIT (1)
CPNS1_RABIT (1)
G1T8H5_RABIT (1)
G1TL08_RABIT (1)
G1SZP6_RABIT (1)
A0A5F9CNA2_RABIT (1)
G1TKV1_RABIT (1)
G1TSW8_RABIT (1)
U3KM54_RABIT (1)
G1SDU8_RABIT (1)
G1SJQ2_RABIT (1)
A0A5F9D7S5_RABIT (1)
G1TEP2_RABIT (1)
G1U207_RABIT (1)
G1SPW1_RABIT (1)
G1SN00_RABIT (1)
G1TN29_RABIT (1)

ENSEMBL ID

ENSG00000170477 (18)
ENSG00000247315 (4)
ENSG00000147251 (4)

CHEBI ID

CHEBI:16015 (31)
CHEBI:17895 (31)
CHEBI:17368 (31)
CHEBI:17596 (30)
CHEBI:17568 (29)
CHEBI:30769 (29)
CHEBI:55328 (27)
CHEBI:16708 (26)
CHEBI:15741 (26)
CHEBI:17154 (26)
CHEBI:17203 (26)
CHEBI:15891 (26)
CHEBI:15971 (26)
CHEBI:16704 (26)
CHEBI:16919 (26)
CHEBI:17295 (26)
CHEBI:30805 (25)
CHEBI:17821 (25)
CHEBI:16467 (25)
CHEBI:18050 (25)
CHEBI:16750 (24)
CHEBI:15756 (24)
CHEBI:17562 (23)
CHEBI:28842 (23)
CHEBI:17015 (23)
CHEBI:16335 (23)
CHEBI:17509 (23)
CHEBI:7916 (23)
CHEBI:17750 (23)
CHEBI:16359 (23)

Metabolite Name

Uracil (38)
L-Tryptophan (35)
Hypoxanthine (35)
L-Histidine (34)
L-Tyrosine (33)
Inosine (33)
L-Proline (32)
Adenine (32)
Taurine (31)
Uridine (31)
Thymine (30)
L-Arginine (30)
Guanine (30)
Creatinine (30)
Creatine (30)
L-Leucine (30)
L-Phenylalanine (30)
Cholic acid (29)
Riboflavin (29)
Guanosine (29)
L-Methionine (29)
L-Threonine (28)
Adenosine (28)
Xanthine (28)
L-Lysine (27)
Palmitic acid (27)
L-Glutamine (27)
L-Valine (27)
Betaine (26)
Choline (26)

First Public Date

2013 (1058)
2016 (922)
2014 (481)
2017 (425)
2015 (400)
2019 (343)
2022 (240)
2020 (158)
2018 (145)
2021 (140)
2024 (128)
2025 (109)
2023 (104)
2026 (95)

Modelling Approach

Constraint-based model (1)

Lab affiliation

Emmy-Noether Research Group Cellular Proteomics and Metabolic Signaling Institute for Diabetes and Obesity Helmholtz Diabetes Center Germany (4)
Key Lab of Integrated Crop Pest Management of Shandong, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China (4)
Shandong University (4)
Tianjin Medical University General Hospital (3)
First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (3)
Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (3)
Agronomy College, Henan Agricultural University, China (3)
Shenzhen People’s Hospital (3)
Department of Biomedical Sciences, University of Sassari, Italy (3)
Zhejiang Academy of Agricultural Sciences (3)
State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China (3)
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China (3)
Shenyang Agricultural University (3)
Shandong Agricultural University (3)
Department of Ophthalmology, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China (2)
Department of Biochemistry and Microbiology, Ghent University, Belgium (2)
Shenzhen Center for Disease Control and Prevention (2)
Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK (2)
College of Life Sciences, University of Dundee (2)
Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. (2)
Qingdao Agricultural University (2)
College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, China (2)
Lanzhou Veterinary Research Institute,Chinese Academy Agricultrural Sciences,China (2)
Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China, 510515 (2)
South China Agricultural University (2)
Inner Mongolia Key Laboratory Of Sheep & Goat Genetics Breeding and Reproduction, Hohhot,China. (2)
Faculty of Medicine and University Hospital of Cologne, Institute of Pathology, University of Cologne, Cologne, Germany (2)
Key Laboratory of Rare and Uncommon Diseases, Department of Microbiology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences (2)
Shandong university of Traditional Chinese Medicine (2)
Institute of Biotechnology, College of Life and Health Sciences, Northeastern University, Shenyang, China (2)

IsPrivate

False (1)

Model Flag

Non Kinetic (1)

Classification

bacteria (282)
fungi (3)
protozoa (3)

Modification

2x(15)N labeled L-lysine (1)
57.02146 (1)
15.99491 (1)
4x(15)N labeled L-arginine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (105)
RNA-seq of coding RNA (32)
ChIP-seq (5)
Comparative genomic hybridization by array (3)
Animal - High-throughput sequencing (2)
ChIP-chip by array (2)
Other (2)
RNA-seq of non coding RNA (2)
Transcription profiling by SAGE (1)
Unknown experiment type (1)
Proteomic profiling by mass spectrometer (1)
Transcription profiling by RT-PCR (1)
Methylation profiling by array (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2022 (2204)
2021 (1620)
2023 (1567)
2024 (1154)
2020 (1147)
2025 (1137)
2019 (745)
2018 (459)
2017 (328)
2015 (232)
2016 (223)
2014 (155)
2013 (130)
2026 (99)
2012 (77)
2011 (46)
2010 (40)
2009 (28)
2008 (25)
2006 (8)
2007 (8)
2005 (5)
2004 (3)
2001 (2)

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Cancer Cell Line Encyclopedia Metabolomics

Not available

ORGANISM(S): Homo sapiens

ST001142 | MetabolomicsWorkbench

RNA-seq of 1019 human cancer cell lines from the Cancer Cell Line Encyclopedia

RNA-seq of 1019 human cancer cell lines from the Broad-Novartis Cancer Cell Line Encyclopedia (http://www.broadinstitute.org/ccle). The original annotation of each cell line to a disease has been checked and manually curated by Expression Atlas (https://www.ebi.ac.uk/gxa/home). Note the original ver...

ORGANISM(S): Homo sapiens

2013-05-31 | E-MTAB-2770 | biostudies-arrayexpress

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

The Cancer Cell Line Encyclopedia (CCLE) is a collaborative effort to generate steady-state large-scale profiling across a collection of nearly a thousand cancer cell lines. Multiple generations of this effort have resulted in a collection of many data types such as RNA expression, mutation annotati...

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

2020-07-27 | MSV000085836 | MassIVE

Cancer Cell Line Encyclopedia (CCLE) Long Read RNA-seq

PRJNA1077632 | ENA

SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE)

This SuperSeries is composed of the following subset Series: GSE36133: Expression data from the Cancer Cell Line Encyclopedia (CCLE) GSE36138: SNP array data from the Cancer Cell Line Encyclopedia (CCLE) Refer to individual Series

ORGANISM(S): Homo sapiens

2012-03-20 | E-GEOD-36139 | biostudies-arrayexpress

The transcription factor encyclopedia.

Not available

S-EPMC3439975 | biostudies-literature

CD-CODE: crowdsourcing condensate database and encyclopedia.

Not available

S-EPMC10172118 | biostudies-literature

Wheat-RegNet: An encyclopedia of common wheat hierarchical regulatory network

PRJNA857711 | ENA

SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE)

PRJNA152953 | ENA