630 - OmicsDI

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Unknown (4166)
Transcriptomics (924)
Genomics (718)
Proteomics (340)
Metabolomics (16)
Models (8)
Methylation profiling (3)
Clinical (2)
Genomic (1)
Other (1)

Organisms

Homo sapiens (448)
Mus musculus (371)
Caenorhabditis elegans (185)
Drosophila melanogaster (90)
Saccharomyces cerevisiae (80)
Clostridioides difficile 630 (31)
Schizosaccharomyces pombe (21)
Arabidopsis thaliana (20)
Yersinia enterocolitica (15)
Escherichia coli (12)
Rattus norvegicus (9)
Helicobacter pylori (8)
Tetrahymena thermophila (6)
Zea mays (6)
Escherichia coli O157:H7 (6)
Salmonella enterica subsp. enterica serovar Typhimurium (6)
Plasmodium falciparum (5)
Danio rerio (5)
Corynebacterium glutamicum (4)
Gossypium hirsutum (3)
synthetic construct (3)
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (3)
Saccharomyces cerevisiae S288C (3)
Francisella tularensis (2)
Bacillus subtilis (2)
Mycolicibacterium smegmatis MC2 155 (2)
Cryptococcus neoformans (2)
Canis lupus familiaris (2)
Gallus gallus (2)
Candida albicans (2)

Organisms

Yersinia enterocolitica (72)
Homo sapiens (36)
Clostridioides difficile 630 (25)
Clostridioides difficile (18)
Mus musculus (15)
Oryza sativa (3)
Solanum tuberosum (2)
Staphylococcus aureus (2)
Bos taurus (2)
Arabidopsis thaliana (2)
Siansivirga zeaxanthinifaciens CC-SAMT-1 (1)
Shewanella sp. W3-18-1 (1)
Salsola sinkiangensis (1)
Saccharopolyspora spinosa (1)
Salvelinus fontinalis (1)
Thlaspi arvense (1)
Lactococcus cremoris (1)
mixed culture metagenome (1)
Phaseolus vulgaris (1)
bacterial mixed DNA library (1)
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (1)
Xenopus laevis (1)
Drosophila melanogaster (1)
Setaria viridis (1)
wood decay metagenome (1)
mouse gut metagenome (1)
Lactiplantibacillus plantarum (1)
Sus scrofa (1)
Zea mays (1)
Escherichia coli (1)

Repository

biostudies-arrayexpress (1330)
pride (311)
ENA (237)
geo (77)
MetaboLights (13)
MassIVE (10)
EGA (7)
BioModels (6)
jPOST (6)
iProX (4)
NODE (3)
ExpressionAtlas (2)
GNPS (2)
Cell Collective (1)
dbGaP (1)
MetabolomicsWorkbench (1)
PMR (1)

Tissue

Cell culture (81)
Permanent cell line cell (20)
Epithelial cell (19)
Liver (10)
Whole body (10)
Brain (9)
Kidney (9)
T cell (8)
Blood (7)
Colon (6)
Embryonic stem cell (6)
Hepatocyte (6)
Plant cell (6)
Seedling (6)
B cell (5)
Cell suspension culture (5)
Fibroblast (5)
Blood cell (4)
Dendritic cell (4)
Erythrocyte (4)
HEK-293T cell (4)
Ovary (4)
Prokaryotic cell (4)
Early embryonic cell (3)
Heart (3)
Leaf (3)
Leukocyte (3)
Umbilical cord (2)
Intestine (1)
Bone marrow (1)

Disease

Normal (14)
Breast cancer (9)
Acute leukemia (7)
Disease free (7)
Colon cancer (6)
Cervix carcinoma (5)
Osteosarcoma (3)
Colorectal Neoplasms (2)
Brain cancer (2)
Brain glioblastoma multiforme (2)
Cardiovascular system disease (2)
Huntington Disease (2)
Malignant neoplasm of ovary (2)
Melanoma (2)
Plasmodium falciparum malaria (2)
Prostate adenocarcinoma (2)
Retinoblastoma (2)
Theileriasis (2)
Follicular lymphoma (1)
Malignant fibrous histiocytoma (1)
Bronchioloalveolar carcinoma of lung (1)
Colorectal cancer (1)
Osteosarcoma (1)
Cancer (1)
Leiomyosarcoma (1)
Gastric cancer (1)
Hepatocellular carcinoma (1)
Carcinoma (1)
Healthy donor tissue (1)
Antibiotic resistance (1)

Technology Type

Mass Spectrometry (312)
Shotgun proteomics (133)
Affinity purification coupled with mass spectrometry proteomics (106)
Bottom-up proteomics (59)
Data-dependent acquisition (44)
Gel-based experiment (23)
Data-independent acquisition (22)
Top-down proteomics (13)
Chemical cross-linking coupled with mass spectrometry proteomics (7)
NMR spectroscopy (6)
Mass spectrometry (5)
SWATH MS (5)
Affinity proteomics (4)
Immunopeptidomics (4)
SRM/MRM (4)
Mass spectrometry assay (2)
DiaPASEF (2)
HDMSE (2)
EI (1)
All-ion fragmentation (1)

Instrument Platform

NextSeq 500 (57)
Illumina NovaSeq 6000 (44)
Illumina HiSeq 2000 (44)
Illumina HiSeq 2500 (41)
Illumina HiSeq 4000 (22)
NextSeq 2000 (15)
Illumina MiSeq (14)
NextSeq 550 (13)
Illumina Genome Analyzer II (10)
Axon GenePix 4000B scanning hardware (8)
Illumina NovaSeq X (6)
Element AVITI (4)
Illumina Genome Analyzer IIx (4)
Agilent G2565BA (3)
Illumina HiSeq 3000 (3)
IEO HPC (2)
PromethION (2)
Axon GenePix4000B (2)
Variable Atmosphere Incubator (2)
HiSeq X Ten (2)
Using NEBNext Ultra II DNA Library (1)
KAPA RNA HyperPrep Kit (1)
Omni ATAC kit (1)
Lightwave (1)
Dell PowerEdge 630 with Intel Xeon E5-2630 processor (8 cores 16 threads) and 94 GB memory running CentOS Linux release 7.5.1804. (1)
PacBio RS II (1)
Genepix 4000A array scanner (1)
Advalytix Slide Booster (1)
454 GS 20 (1)
Anaerobic workstation with airlock (1)

Publication Date

2013 (210)
2015 (173)
2012 (142)
2010 (138)
2014 (125)
2016 (119)
2023 (88)
2026 (85)
2025 (85)
2011 (78)
2021 (72)
2024 (70)
2022 (66)
2008 (54)
2020 (52)
2018 (43)
2019 (42)
2009 (36)
2006 (25)
2007 (23)
2017 (22)
2005 (10)
2004 (2)

UNIPROT ID/AC

Q180S4 (2)
Q189W2 (2)
Q185S2 (2)
Q18D63 (2)
Q186Q4 (2)
Q188F3 (2)
Q180C1 (2)
Q185P1 (2)
Q18C47 (2)
Q184J4 (2)
Q182U5 (2)
Q17ZW9 (2)
Q18CA4 (2)
Q189S4 (2)
Q189R6 (2)
Q189R2 (2)
Q183X2 (2)
Q189R4 (2)
Q18CJ2 (2)
Q181D7 (2)
Q188A1 (2)
Q180R8 (2)
Q182B6 (2)
Q181K1 (2)
Q181I0 (2)
Q188T6 (2)
Q187E6 (2)
Q183H3 (2)
Q186K9 (2)
Q180P4 (2)

CHEBI ID

CHEBI:15366 (6)
CHEBI:30751 (5)
CHEBI:17750 (5)
CHEBI:30769 (5)
CHEBI:4167 (4)
CHEBI:27266 (4)
CHEBI:30768 (4)
CHEBI:15891 (4)
CHEBI:18237 (4)
CHEBI:15741 (4)
CHEBI:32816 (4)
CHEBI:17268 (4)
CHEBI:15428 (4)
CHEBI:18012 (4)
CHEBI:16449 (4)
CHEBI:16737 (4)
CHEBI:16919 (4)
CHEBI:15354 (4)
CHEBI:412516 (3)
CHEBI:18186 (3)
CHEBI:17790 (3)
CHEBI:17170 (3)
CHEBI:24898 (3)
CHEBI:15344 (3)
CHEBI:18123 (3)
CHEBI:16857 (3)
CHEBI:16196 (3)
CHEBI:7916 (3)
CHEBI:16977 (3)
CHEBI:78320 (3)

Metabolite Name

Valine (5)
Formate (4)
Glycine (4)
Betaine (4)
Taurine (4)
Alanine (4)
Isoleucine (4)
Creatine (4)
HMF (3)
Acetate (3)
Choline (3)
Threonine (3)
Succinate (3)
Glucose (3)
Pyruvate (3)
Creatinine (3)
Lanosterol (2)
Acetoacetic acid (2)
Arabitol (2)
Methanol (2)
Histidine (2)
L-leucine (2)
Leucine (2)
Lactose (2)
Myo-Inositol (2)
Hippurate (2)
L-alanine (2)
Glycerol (2)
Dimethylamine (2)
Glycolic acid (2)

First Public Date

2014 (28)
2024 (27)
2025 (24)
2020 (22)
2026 (21)
2023 (20)
2021 (20)
2022 (16)
2016 (12)
2018 (11)
2017 (11)
2015 (10)
2013 (10)
2019 (5)

Modelling Approach

Ordinary differential equation model (2)
Metabolic network (1)
Logical model (1)
Constraint-based model (1)

Study status

Not provided (1)
Recruiting (1)

Lab affiliation

University of Oxford (11)
Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology (7)
Cellzome (5)
Associate Professor, Department of Biology, Massachusetts Institute of Technology and Whitehead Institute of Biomedical Research (4)
Biochemistry Center Heidelberg, University of Heidelberg, Germany (4)
Faculty of Biology, Technion - Israel Institute of Technology (4)
University of Greifswald, Institute of Microbiology, Department of Microbial Physiology and Molecular Biology (4)
Cancer Science Institute of Singapore, National University of Singapore (3)
Crick-GSK LinkLabs, UK (3)
Department of Chemistry, University of Washington (3)
Signalling ISP, Babraham Institute, Cambridge, UK (3)
University of Oxford University of Dundee (3)
Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands (2)
Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald (2)
Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands (2)
ETH Zürich Institute of Molecular Systems Biology Otto-Stern-Weg 3 8093 Zürich Switzerland (2)
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. (2)
Head of the Curie Institute Mass Spectrometry Platform (2)
Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany (2)
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria. (2)
Ist. G. Gaslini (2)
Molecular Genetics, RPTU Kaiserslautern, Germany (2)
Molecular Plant Biology, University of Turku (2)
Vanderbilt University (2)
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Biology, Cambridge, MA, USA (2)
1 National Centre for Scientific Research “Demokritos”, Agia Paraskevi, Attica, Greece 2 Department of Chemistry, National and Kapodistrian University of Athens, Greece (1)
1. Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. 2. Research Centre for Extracellular Vesicles, La Trobe University, Victoria, Australia. (1)
1.MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK 2.CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK (1)
1.Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA, USA. 2. Department of Pediatrics, Harvard Medical School, Boston, MA, USA. (1)
1Department of Molecular Biology & 2LSI Genomics, Princeton University (1)

Keyword

Adenocarcinoma, (1)
Colorectal tumors, (1)
Endogenous porphyrins, (1)
Fluorescence, (1)
Tumor markers. (1)

IsPrivate

False (6)

Model Flag

Non Kinetic (3)

Submitter Keywords

FROG (1)

Classification

bacteria (119)

Modification

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

Study type

ChIP-seq (431)
ChIP-chip by tiling array (198)
Transcription profiling by array (171)
RNA-seq of coding RNA (130)
ChIP-chip by array (94)
Other (75)
RNA-seq of non coding RNA (27)
ATAC-seq (23)
Comparative genomic hybridization by array (17)
RIP-seq (13)
Cell line - High-throughput sequencing (12)
CLIP-seq (12)
DNA-seq (12)
Hi-C (11)
RNA-seq of coding RNA from single cells (11)
Methylation profiling by high throughput sequencing (11)
Unknown experiment type (9)
Animal - High-throughput sequencing (9)
Methylation profiling by array (9)
Ribo-seq (7)
Transcription profiling by tiling array (6)
Proteomic profiling by array (6)
RNA-seq of total RNA (5)
MNase-seq (4)
High-throughput sequencing (4)
Single nucleus RNA sequencing (3)
GRO-seq (2)
MicroRNA profiling by high throughput sequencing (2)
4C (2)
ScATAC-seq (2)

Release Date

2022 (484)
2021 (442)
2023 (408)
2025 (400)
2020 (370)
2024 (351)
2015 (309)
2013 (303)
2018 (291)
2019 (288)
2016 (286)
2014 (276)
2012 (228)
2017 (221)
2010 (197)
2011 (142)
2008 (107)
2009 (86)
2026 (84)
2007 (60)
2006 (48)
2005 (31)
2002 (20)
2004 (15)
2000 (15)
2003 (14)
1998 (8)
2001 (5)
1999 (4)
1997 (2)

Location

Spain (1)
Italy (1)
Belgium (1)
Germany (1)
United States (1)

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Clostridioides difficile 630

Clostridioides difficile 630 Genome sequencing

PRJNA929299 | ENA

Clostridioides difficile 630

Clostridioides difficile 630 Genome sequencing

PRJNA275406 | ENA

Koivumäki, Korhonen, Tavi 2011 Atrial AP model

Model of the human atrial AP by Koivumäki, Korhonen & Tavi, 2011

630 | Physiome Model Repository

Clostridioides difficile 630

Clostridioides difficile 630 Genome sequencing

PRJNA354635 | ENA

Clostridium difficile strain 630 heat stress experiment

Transcriptomic analysis of C. difficile strain 630 subjected to a clinically relevant heat stress (41M-BM-0C ) and compared to unstressed cells (37M-BM-0C ). Heat stress was induced in biological triplicate broth cultures in the early exponential phase (D650nm=0.3) of growth and cells were harveste...

ORGANISM(S): Clostridium difficile 630

2012-04-19 | E-GEOD-37442 | biostudies-arrayexpress

Transcription profiling by array of temporal gene expression in germinating Clostridium difficile 630 endospores

Clostridium difficile is the leading cause of hospital acquired diarrhoea in industrialised countries. Under conditions that are not favourable for growth, the pathogen produces metabolically dormant endospores via asymmetric cell division. These are extremely resistant to both chemical and physical...

ORGANISM(S): Clostridium difficile

2013-03-16 | E-BUGS-145 | biostudies-arrayexpress

Clostridioides difficile 630

Clostridioides difficile 630 Raw sequence reads

PRJNA949940 | ENA

Clostridioides difficile 630

Clostridioides difficile 630 Genome sequencing and assembly

PRJNA997943 | ENA

Grad-seq Clostridium difficile 630

Grad-seq in Clostridium difficile 630. Cell lysate is analyzed in a gradient and fractionated into 21 fractions which are analysed for proteins by MS and for transcripts by RNA-sequencing.

ORGANISM(S): Peptoclostridium difficile (strain 630) (Clostridium difficile)

2021-05-12 | PXD022525 | Pride

Clostridium Grad-seq

Clostridioides difficile 630

Clostridium difficile strain 630 heat stress experiment

PRJNA160179 | ENA

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