Richard C C - OmicsDI

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Unknown (3063)
Transcriptomics (1484)
Genomics (552)
Proteomics (529)
Metabolomics (100)
Models (18)
Genomic (17)
Other (6)
Multiomics (3)
Methylation profiling (1)

Organisms

Homo sapiens (1206)
Mus musculus (548)
Arabidopsis thaliana (74)
Rattus norvegicus (65)
Caenorhabditis elegans (59)
Drosophila melanogaster (29)
Danio rerio (25)
Saccharomyces cerevisiae (24)
Bos taurus (20)
Gallus gallus (16)
Macaca mulatta (13)
Canis lupus familiaris (10)
Medicago truncatula (10)
Staphylococcus aureus (9)
Salmo salar (9)
Candida albicans (7)
Trypanosoma brucei (6)
Halobacterium salinarum (6)
Escherichia coli (6)
Sus scrofa (6)
Ascaris suum (6)
Macaca fascicularis (5)
Clavispora lusitaniae (5)
Hypomesus transpacificus (5)
Xenopus laevis (5)
Oryza sativa (5)
Pimephales promelas (4)
Mycobacterium tuberculosis (4)
cellular organisms (3)
Clostridioides difficile (1)

Organisms

Homo sapiens (8)
Mus musculus (8)
Ascaris suum (4)
Candida albicans (2)
Caenorhabditis elegans (2)
Streptococcus mutans (1)
Bos taurus (1)

Repository

biostudies-arrayexpress (1618)
EGA (390)
pride (278)
MassIVE (145)
PeptideAtlas (66)
GNPS (56)
MetaboLights (44)
ENA (29)
PanoramaPublic (19)
BioModels (18)
dbGaP (17)
PAXDB (9)
GPMDB (6)
jPOST (6)
iProX (5)
geo (3)

Tissue

Cell culture (45)
Plant cell (20)
Leaf (17)
Brain (14)
Permanent cell line cell (10)
Plasma Non-glyco (9)
Liver (8)
Blood serum (7)
Colon (7)
Blood plasma (6)
Epithelial cell (6)
Kidney (6)
Seedling (6)
T cell (6)
Whole body (6)
B cell (5)
Blood (5)
Heart (5)
Ovary (5)
Small intestine (5)
Spleen (5)
Cell suspension culture (4)
Fibroblast (4)
Root (4)
Stomach (4)
Urine (4)
Breast (3)
Duodenum (3)
Eye (1)
Others (1)

Disease

Normal (5)
Parkinson's disease (4)
Alzheimer's disease (3)
Colon adenocarcinoma (3)
Wilms tumour (3)
Porphyria NOS (2)
Acute myeloid leukemia (2)
Cataract (1)
Type 1 diabetes mellitus (1)
Inoculated with P. syringae pv. tomato strain DC3000 + avrRps4 (1)
Aviremic HIV (1)
Septic peritonitis (1)
Vitamin B12 deficiency (1)
Papillary renal cell carcinoma (1)
Extra-adrenal sympathetic paraganglioma (1)
DNA damage (1)
Inflammatory breast carcinoma (1)
Systemic lupus erythematosus (1)
T. circumcincta infection (1)
Schizophrenia (1)
Benign Prostatic Hyperplasia (1)
Kaposi's sarcoma (1)
Primary tumor (1)
Slightly obese (1)
Colon carcinoma (1)
Choriocarcinoma (1)
Neurologically healthy control (1)
Normal (1)
Papillary thyroid carcinoma (1)
Acute Myeloid Leukemia (1)

Technology Type

Illumina HiSeq 2000 (11)
Illumina 15K (8)
Illumina Genome Analyzer II (5)
Affymetrix 6.0 (2)
Illumina HiSeq 2000, Illumina_2.5M (2)
AB 5500 Genetic Analyzer, Ion Torrent PGM (1)
AB SOLiD 4 System, Illumina HiSeq 2500, Illumina HiSeq 2000, AB SOLiD System 3.0 (1)
ABI_SOLID, Illumina Genome Analyzer IIx, Affymetrix_GenomeWide_SNP6.34 (1)
Affymetrix 6.0, Illumina Genome Analyzer II (1)
Affymetrix 6.0, Illumina_670k - Illuminus, Illumina 1.2M (1)
ILLUMINA, Illumina HiSeq 2000 (1)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina 1.2M, Affymetrix 6.0 (1)
Illumina 1.2M, Affymetrix 6.0, Affymetrix 6.0 - CHIAMO (1)
Illumina 1.2M, Illumina 610K Quad, Affymetrix 6.0 (1)
Illumina 2.5M, Illumina HiSeq 2000 (1)
Illumina CytoSNP, Illumina HumanOmni2.5, ILLUMINA, Illumina 450k, Illumina HiSeq 2000 (1)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (1)
Illumina HiSeq 1000, Ion Torrent PGM, Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2000, ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 2000, Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2000, Illumina HumanOmni2-5M-8v1-1_B (1)
Illumina HiSeq 2000, Illumina HumanOmni2-5_8v1_A (1)
Illumina HiSeq 2000, Illumina Infinium HumanMethylation450 BeadChip, Affymetrix expression array, ILLUMINA (1)
Illumina HiSeq 2000, Illumina MiSeq (1)
Illumina HiSeq 2000, unknown (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2500, Illumina HiSeq 2000 (1)
Illumina HiSeq 2500, Illumina MiSeq (1)
Illumina HumanCNV370, Illumina HumanHap 300 v2 Duo, Taqman and sequencing, Illumina Human660W-Quad (1)

Instrument Platform

Illumina HiSeq 2500 (26)
Illumina HiSeq 2000 (25)
Illumina NovaSeq 6000 (19)
Illumina HiSeq 4000 (13)
NextSeq 500 (9)
Illumina Genome Analyzer IIx (4)
Scanning hardware (4)
Axon GenePix 4000B scanning hardware (3)
Vortex (3)
NextSeq 2000 (3)
BGISEQ-500 (3)
Illumina MiSeq (3)
Illumina HiSeq 3000 (2)
NEXTflex Small-RNA Seq kit v3 (Perkin Elmer) & NEXTflex Rapid XP DNA-seq kit v2 (Perkin Elmer) (1)
Direct-zol RNA microprep kit (Zymo Research), LabChip RNA pico sensitivity assay, Perkin Elmer & Nucleospin RNA kit (Macherey Nagel) (1)
PALM type 4 microscope (Zeiss) (1)
FastPrep-24 5G bead beater, Qubit Fluorometer (1)
12 well TC-treated plate, LETs buffer, dry ice (1)
Lab Chip GX touch HT (Perkin Elmer) (1)
TriZol reagent (1)
GeneChip® Scanner 3000 7G (Affymetrix) (1)
Lightwave (1)
Agilent DNA Microarray Scanner Model #G2565BA (1)
Fluidic Station 450 (1)
IScan (1)
GCS3000 (1)
Axon 4000B scanner (1)
Anaerobic workstation with airlock (1)
Ultracentrifuge (1)
Picopure RNA kit (1)

Publication Date

2013 (252)
2012 (205)
2015 (201)
2014 (190)
2010 (181)
2016 (165)
2011 (165)
2008 (120)
2007 (76)
2024 (72)
2023 (70)
2009 (67)
2018 (65)
2019 (64)
2022 (62)
2021 (58)
2026 (50)
2020 (46)
2025 (45)
2017 (42)
2006 (26)
2005 (12)
2004 (10)

UNIPROT ID/AC

Q9GRG6 (5)
A5ACR7_VITVI (5)
A5ADJ5_VITVI (5)
A5ADV7_VITVI (5)
A5AE63_VITVI (5)
A5AEB4_VITVI (5)
A5AEH1_VITVI (5)
A5AEI0_VITVI (5)
A5AFH3_VITVI (5)
A5AFX4_VITVI (5)
A5AGD5_VITVI (5)
A5AGN5_VITVI (5)
A5AHJ5_VITVI (5)
A5AHY0_VITVI (5)
A5AJ83_VITVI (5)
A5AJY2_VITVI (5)
A5AKD8_VITVI (5)
A5AL04_VITVI (5)
A5ALB2_VITVI (5)
A5ALT5_VITVI (5)
A5ALV6_VITVI (5)
A5AML5_VITVI (5)
A5ANR7_VITVI (5)
A5ANX3_VITVI (5)
A5AP38_VITVI (5)
A5APB9_VITVI (5)
A5APR3_VITVI (5)
A5AQ47_VITVI (5)
P05067 (1)
P37840 (1)

ENSEMBL ID

ENSG00000229353 (6)
ENSG00000170477 (4)
ENSMUSG00000072849 (1)
ENSMUSG00000076514 (1)
ENSMUSG00000076532 (1)
ENSMUSG00000076562 (1)
ENSMUSG00000076668 (1)
ENSMUSG00000076695 (1)
ENSMUSG00000093894 (1)
ENSMUSG00000093896 (1)
ENSMUSG00000094075 (1)
ENSMUSG00000094194 (1)
ENSMUSG00000094356 (1)
ENSMUSG00000094502 (1)
ENSMUSG00000094509 (1)
ENSMUSG00000094546 (1)
ENSMUSG00000094652 (1)
ENSMUSG00000094689 (1)
ENSMUSG00000094797 (1)
ENSMUSG00000095416 (1)
ENSMUSG00000095442 (1)
ENSMUSG00000095753 (1)
ENSMUSG00000096326 (1)
ENSMUSG00000096833 (1)
ENSMUSG00000098557 (1)
ENSMUSG00000098814 (1)
ENSMUSG00000103290 (1)
ENSMUSP00000141097 (1)

CHEBI ID

CHEBI:16027 (17)
CHEBI:17234 (15)
CHEBI:15422 (8)
CHEBI:16761 (8)
CHEBI:13389 (6)
CHEBI:14336 (6)
CHEBI:15361 (6)
CHEBI:15379 (6)
CHEBI:16526 (6)
CHEBI:16908 (6)
CHEBI:17138 (6)
CHEBI:17754 (6)
CHEBI:17794 (6)
CHEBI:18021 (6)
CHEBI:28874 (6)
CHEBI:40595 (6)
CHEBI:4170 (6)
CHEBI:57642 (6)
CHEBI:16474 (5)
CHEBI:17842 (5)
CHEBI:18009 (5)
CHEBI:35490 (5)
CHEBI:48928 (5)
CHEBI:58121 (5)
CHEBI:58273 (5)
CHEBI:28757 (2)
CHEBI:33942 (2)
CHEBI:15858 (1)
CHEBI:22984 (1)
CHEBI:26216 (1)

Metabolite Name

Glycine (10)
Hypoxanthine (9)
Leucine (9)
Alanine (8)
Methionine (8)
Arginine (7)
Choline (7)
Creatinine (7)
Histidine (7)
Inosine (7)
Lysine (7)
Phenylalanine (7)
Serine (7)
Tyrosine (7)
Xanthine (7)
Adenosine (6)
Asparagine (6)
Aspartate (6)
Creatine (6)
Cytidine (6)
Glucose (6)
Glutamate (6)
Glutamine (6)
Guanine (6)
Guanosine (6)
Isoleucine (6)
Ornithine (6)
Proline (6)
Threonine (6)
Tryptophan (6)

First Public Date

2014 (9)
2013 (6)
2024 (3)
2022 (3)
2020 (2)
2017 (2)
2016 (2)
2026 (1)
2015 (1)

Modelling Approach

Ordinary differential equation model (16)
Mathematical model (1)
Other (1)

Lab affiliation

Proteomics facility, Central Science Laboratory, University of Tasmania (25)
Department of Biological Sciences, University of Alberta (5)
Systems Inflammation group, Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Norway (4)
Biology department, Washington University in Saint Louis, Saint Louis, MO, USA (3)
Department of Molecular & Clinical Cancer Medicine Institute of Systems, Molecular & Integrative Biology University of Liverpool (3)
Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy,Chicago,IL,USA Richard and Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering,Chicago, IL,USA University of Illinois Cancer Center,Chicago, IL,USA (3)
Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria Phone: +43 1 79044 9850 http://www.gmi.oeaw.ac.at (3)
Head of the Curie Institute Mass Spectrometry Platform (3)
Utrecht University (3)
1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland 2 Faculty of Science, University of Zurich, Zurich, Switzerland (2)
Center for Immunity and Immunotherapies, Seattle Children's Research Institute. Department of Pediatrics, University of Washington. Seattle, WA USA (2)
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria (2)
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria (2)
Department of Biology, Washington University in St. Louis (2)
Department of Biology,Washington University in St. Louis (2)
Facility Manager, Proteomics Mass Spectrometry, Central Science Laboratory, University of Tasmania (2)
IMBA - Institute of Molecular Biotechnology Dr. Bohrgasse 3 1030 Vienna Austria (2)
IMBA and Medical University of Vienna (2)
IMP, Vienna Biocenter, Vienna, Austria (2)
Institute of Metabolic Science, University of Cambridge (2)
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria. (2)
Laboratory of Toxinology, FIOCRUZ, Brazil (2)
Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (2)
Massachusetts Institute of Technology (2)
Metabolic Research Laboratories, University of Cambridge (2)
Oceanography, University of Washington, USA (2)
Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria (2)
University of Wisconsin School of Medicine and Public Health (2)
Wellcome Trust MRC Institute of Metabolic Science (2)
Wilmer Eye Institute, Smith Building, M015, 400 N. Broadway, Baltimore, MD 21287 (2)

IsPrivate

False (18)

Model Flag

Non Miriam (1)

Submitter Keywords

Machine Learning Model (1)

Classification

helminths (4)
fungi (2)
bacteria (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (2)
Not available (2)
0.984 (1)
15.99491 (1)
57.02146 (1)

Study type

Transcription profiling by array (1011)
RNA-seq of coding RNA (187)
ChIP-seq (112)
Comparative genomic hybridization by array (59)
Methylation profiling by array (47)
Unknown experiment type (22)
RNA-seq of non coding RNA (21)
ChIP-chip by tiling array (20)
Other (19)
Genotyping by array (16)
Methylation profiling by high throughput sequencing (16)
ChIP-chip by array (14)
RNA-seq of coding RNA from single cells (9)
Transcription profiling by tiling array (7)
Transcription profiling by SAGE (5)
RNAi profiling by array (5)
DNA-seq (5)
RNA-seq of total RNA (5)
Animal - High-throughput sequencing (4)
Cell line - High-throughput sequencing (4)
MicroRNA profiling by array (4)
Transcription profiling by RT-PCR (3)
Baseline (2)
MicroRNA profiling by high throughput sequencing (2)
Genotyping by high throughput sequencing (2)
Cell line - Single-cell sequencing (1)
RNA-seq of non coding RNA from single cells (1)
Differential (1)
One-color microarray (1)
Human - Single-cell sequencing (1)

Release Date

2021 (364)
2022 (344)
2023 (313)
2013 (305)
2025 (302)
2020 (283)
2014 (274)
2015 (273)
2012 (269)
2024 (255)
2016 (242)
2010 (227)
2019 (220)
2011 (214)
2018 (208)
2017 (140)
2008 (133)
2009 (92)
2007 (88)
2026 (55)
2006 (36)
2005 (19)
2004 (11)
2002 (4)
2001 (4)
2003 (3)
1997 (2)
1999 (1)

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Hepatitis C Antiviral Long-term Treatment Against Cirrhosis (HALT-C)

Reprinted from http://www.haltctrial.org/

Purpose

The Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial is a randomized controlled trial designed to evaluate the safety and efficacy of long-term use of pegylated inte...

phs000430 | dbGaP

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Multiple regulatory elements distant to their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functi...

EGAS00001001085 | EGA

Hepatitis C Antiviral Long-term Treatment Against Cirrhosis (HALT-C)

Reprinted from http://www.haltctrial.org/

Purpose

The Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial is a randomized controlled trial designed to evaluate the safety and efficacy of long-term use of pegylated inte...

phs000430.v1.p1 | EGA

Transcription profiling of mouse fibroblast cells transfected with zinc-inducible C/EBP expression vectors identifies Per2 as a gene implicated in myeloid leukemia

The zinc-inducible C/EBP expression vectors pMTa, pMTb, pMTd and pMTe were constructed by cloning the human C/EBPa, C/EBPb, C/EBPd and C/EBPe cDNAs, respectively, into the pMTCB6+ vector. NIH 3T3 cells were transfected with zinc-inducible C/EBP vectors as well as control empty vector using the GeneP...

ORGANISM(S): Mus musculus

2007-12-04 | E-GEOD-2188 | biostudies-arrayexpress

Transcription profiling of mouse NFI-C knock out embryonic fibroblasts

The Nuclear Factor I C (NFI-C) transcription factor has been implicated in TGF-Î² signaling, extracellular matrix deposition and skin appendage pathologies. We performed a global gene expression analysis in NFI-C-/- and wild-type embryonic primary murine fibroblasts. This indicated that NFI-C acts m...

ORGANISM(S): Mus musculus

2009-11-15 | E-GEOD-15871 | biostudies-arrayexpress

ena-DATASET-ICR-PTGT-05-02-2015-11:21:41:591-6 - samples

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.

EGAD00001001243 | EGA

Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-Seq

Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription ...

ORGANISM(S): Mus musculus

2010-04-02 | E-GEOD-20530 | biostudies-arrayexpress

Induction of hepatocellular carcinoma through activation of stromal cells in Pdgf-c transgenic mice

Liver cirrhosis is a strong risk factor for the development of hepatocellular carcinoma (HCC), yet the mechanisms by which cirrhosis predisposes patients to tumorigenesis are not well understood. Transgenic mice expressing platelet-derived growth factor C (Pdgf-c) under the control of the albumin pr...

ORGANISM(S): Mus musculus

2014-05-12 | E-GEOD-38199 | biostudies-arrayexpress

Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-chip

ORGANISM(S): Mus musculus

2010-04-02 | E-GEOD-20529 | biostudies-arrayexpress

Transcription profiling of male Fech mutant BALB/c mouse livers vs male control BALB/c livers

Comparison of gene expression in livers of male Fech mutant BALB/c mouse with livers of male control BALB/c

ORGANISM(S): Mus musculus

2005-10-14 | E-MEXP-189 | biostudies-arrayexpress

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