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Unknown (757)
Transcriptomics (109)
Proteomics (67)
Genomics (63)
Metabolomics (30)
Other (1)

Organisms

Homo sapiens (67)
Rattus norvegicus (65)
Mus musculus (50)
Mycolicibacterium smegmatis MC2 155 (5)
Drosophila melanogaster (5)
Schizosaccharomyces pombe (4)
Glycine max (4)
Saccharomyces cerevisiae (4)
Arabidopsis thaliana (4)
Streptomyces venezuelae (3)
Sus scrofa (3)
Lolium perenne (2)
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Oryza sativa Japonica Group (2)
Danio rerio (2)
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Mesorhizobium metallidurans STM 2683 (1)
Drosophila sechellia (1)
Capra hircus (1)
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Pseudomonas fluorescens (1)
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Triticum aestivum (1)
Escherichia coli str. K-12 substr. MG1655 (1)
Rattus norvegicus (1)

Repository

biostudies-arrayexpress (168)
pride (65)
MetaboLights (30)
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Tissue

Cell culture (17)
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Disease

Porphyria NOS (2)
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Not Available (1)
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Semantic dementia (1)
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Head and neck squamous cell carcinoma (1)
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COVID-19 (1)
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Parkinson's disease (1)
Glioblastoma (1)
Neuroblastoma (1)

Technology Type

Mass Spectrometry (65)
Shotgun proteomics (38)
Mass spectrometry (24)
Gel-based experiment (19)
Affinity purification coupled with mass spectrometry proteomics (11)
NMR spectroscopy (10)
Data-dependent acquisition (3)
SWATH MS (3)
Bottom-up proteomics (2)
Illumina HiSeq 2500 (1)
DiaPASEF (1)
SRM/MRM (1)
Top-down proteomics (1)
Data-independent acquisition (1)

Instrument Platform

Illumina HiSeq 2000 (13)
Illumina HiSeq 2500 (10)
Liquid Chromatography MS - positive - reverse phase (10)
Liquid Chromatography MS - negative - reverse phase (9)
Illumina HiSeq 4000 (7)
NextSeq 500 (6)
Illumina Genome Analyzer II (5)
NextSeq 550 (5)
Illumina NovaSeq 6000 (5)
Varian (4)
Nuclear Magnetic Resonance (NMR) - (4)
Exactive (Thermo Scientific) (4)
Illumina Genome Analyzer IIx (3)
Liquid Chromatography MS - negative - hilic (3)
Liquid Chromatography MS - positive - hilic (3)
Axon GenePix 4000B scanning hardware (2)
Illumina NovaSeq X (2)
Gas Chromatography MS - (2)
10X Genomics Chromium (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)
2100 Bioanalyzer (Agilent, CA, USA), Qubit 2.0 (Invitrogen, Germany) (1)
BD Influx (1)
GenePix Professional 4200A [Axon Instruments] (1)
NA (1)
NextSeq 2000 (1)
Illumina HiSeq 1500 (1)
Illumina HiSeq 3000 (1)
Instrument (1)
Q Exactive (1)
LTQ Orbitrap (1)

Publication Date

2013 (30)
2021 (26)
2015 (24)
2016 (20)
2014 (19)
2012 (17)
2019 (16)
2018 (16)
2020 (14)
2010 (13)
2023 (12)
2025 (11)
2022 (11)
2017 (9)
2026 (8)
2024 (6)
2011 (6)
2006 (3)
2009 (2)
2005 (2)

CHEBI ID

CHEBI:28044 (13)
CHEBI:15741 (11)
CHEBI:17750 (10)
CHEBI:15428 (10)
CHEBI:16919 (10)
CHEBI:15891 (10)
CHEBI:24898 (9)
CHEBI:16449 (9)
CHEBI:18237 (9)
CHEBI:16737 (9)
CHEBI:15354 (9)
CHEBI:27266 (8)
CHEBI:26271 (8)
CHEBI:25094 (8)
CHEBI:26986 (8)
CHEBI:16811 (8)
CHEBI:25017 (8)
CHEBI:27897 (8)
CHEBI:30769 (8)
CHEBI:15366 (7)
CHEBI:22660 (7)
CHEBI:18186 (7)
CHEBI:17234 (7)
CHEBI:17822 (7)
CHEBI:15611 (7)
CHEBI:16704 (7)
CHEBI:17596 (7)
CHEBI:78320 (6)
CHEBI:28300 (6)
CHEBI:22653 (6)

Metabolite Name

Choline (5)
Creatinine (5)
Phenylalanine (5)
Isoleucine (5)
Creatine (4)
Tyrosine (4)
Valine (4)
Methionine (4)
Alanine (4)
Glycine (4)
Tryptophan (4)
Creatine (4)
Taurine (4)
Creatinine (3)
Lysine (3)
Histidine (3)
Inosine (3)
Betaine (3)
Choline (3)
Leucine (3)
Proline (3)
Phenylalanine (3)
Taurine (3)
Betaine (3)
Glycerol (3)
Acetic acid (3)
L-Leucine (3)
Threonine (3)
Succinate (3)
Sarcosine (3)

First Public Date

2020 (1)

Modification

N6 (2)
N6-dimethyl-L-lysine (2)
2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)

Study type

RNA-seq of coding RNA (62)
ChIP-seq (47)
Transcription profiling by array (17)
Methylation profiling by high throughput sequencing (8)
Other (7)
RNA-seq of coding RNA from single cells (6)
RNA-seq of non coding RNA (5)
MicroRNA profiling by high throughput sequencing (3)
Cell line - High-throughput sequencing (2)
DNA-seq (2)
RNA-seq of total RNA (2)
Animal - Single-cell sequencing (1)
High-throughput sequencing (1)
Transcription profiling by RT-PCR (1)
Bisulfite-seq (1)
RIP-seq (1)

Release Date

2021 (88)
2022 (76)
2024 (73)
2015 (72)
2023 (66)
2016 (66)
2025 (63)
2020 (56)
2019 (56)
2013 (55)
2012 (53)
2014 (46)
2017 (37)
2018 (33)
2011 (25)
2010 (22)
2009 (13)
2026 (11)
2006 (5)
2007 (3)
2005 (2)
2008 (2)
2002 (1)
2001 (1)

Lab affiliation

UAB CCC MS Proteomics Facility (2)
Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (2)
ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium (1)
Cambridge Centre for Proteomics University of Cambridge (1)
Professor of Molecular Biology, University of Dundee (1)
King's College London School of Cardiovascular and Metabolic Medicine & Sciences James Black Centre 125 Coldharbour Lane, London, SE5 9NU (1)
Johns Hopkins Bloomberg School of Public Health (1)
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium (1)
National Heart & Lung Institute, Imperial College London, London, UK (1)
University Magdeburg, Medical School, Institute of Exptl. Internal Medicine, Leipzigerstr. 44, 39120 Magdeburg, Germany (1)
Functional Urology Research Lab, DBMR, University of Bern, 3008 Bern, Switzerland (1)
Department of Translational Research in Psychiatry, Proteomics Core Unit, Max Planck Institute of Psychiatry, Germany (1)
German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, München, Germany (1)
Highly Specialised Mitochondrial Diagnostic Laboratory, Wellcome Centre for Mitochondrial Research, Newcastle University, UK (1)
Institute of Biochemistry II Goethe University School of Medicine Germany (1)
Kennesaw State University (1)
Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Switzerland (1)
Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX USA (1)
Cell Biology, Faculty of Science, Utrecht University (1)
Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia (1)
Department of Microbiology Faculty of Agriculture and Forestry University of Helsinki Latokartanonkaari 7 Helsinki Finland (1)
Director of the UAB CCC Mass Spectrometry Shared Facility (1)
Director UAB CCC Mass Spectrometry Shared Facility (1)
Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic (1)
University of Victoria, Department of Mechanical Engineering, PO Box 1700 STN CSC, Victoria, BC, V8W 2Y2, Canada (1)
Department of Radiation Oncology Winthrop P. Rockefeller Cancer Institute University of Arkansas for Medical Sciences, USA (1)
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia. (1)
Tobias B. Dansen, Ph.D. University Medical Center Utrecht Dept. Molecular Cancer Research, Universiteitsweg 100, STR 3.203 3584 CG Utrecht, The Netherlands (1)
School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, Bristol, BS81TD (1)
Division of Hematology/Oncology Boston Children's Hospital Boston, MA, USA (1)

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Changes to SUMO-modified proteome and total cellular proteome during EBV ractivation in AGS gastric carcinoma cells

To monitor changes to cellular and viral SUMO-modified proteins during EBV reactivation. SUMO1 and SUMO2 conjugates were studied using KGG mutant forms of SUMO and GG-K specific antibody enrichment of SUMO modified peptides. Time-points of 12h and 24h post-reactivation were monitored. Total cellular...

ORGANISM(S): Homo sapiens (Human)

2023-06-19 | PXD034631 | Pride

Sumo epstein-barr virus ebvhuman herpes virus 4 hhv4

De-obstruction of bladder outlet in humans reverses organ remodeling

Bladder outlet obstruction (BOO) causes lower urinary tract symptoms and objectifiable urodynamic changes in bladder function. We carried out an integrated transcriptome and proteome analysis of bladder samples from male patients with BOO before and 3 months after de-obstruction surgery (transurethr...

ORGANISM(S): Homo sapiens (Human)

2024-05-21 | PXD044777 | Pride

Remodelling Bladder Fibrosis Outlet obstruction

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

DNA methylation is an epigenetic modification associated with transcriptional repression of promoters and is essential for mammalian development. Establishment of DNA methylation is mediated by the de novo DNA methyltransferases DNMT3A and DNMT3B, whereas DNMT1 ensures maintenance of methylation thr...

ORGANISM(S): Mus musculus

2015-01-20 | E-GEOD-57412 | biostudies-arrayexpress

Specificity quantification of Glucocorticoid receptor binding using high-throughput sequencing

In this work, we used our recently developed method Spec-seq to characterize the binding specificity of Glucocorticoid receptor in vitro. This GR Spec-seq experiment has been run twice separately (Dec 2014 and Mar 2015) with different library compositions. The basic workflow is the same as our previ...

ORGANISM(S): Homo sapiens

2015-07-01 | E-GEOD-69386 | biostudies-arrayexpress

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

This SuperSeries is composed of the SubSeries listed below. DNA methylation is an epigenetic modification associated with transcriptional repression of promoters and is essential for mammalian development. Establishment of DNA methylation is mediated by the de novo DNA methyltransferases DNMT3A and...

ORGANISM(S): Mus musculus

2015-01-22 | E-GEOD-57413 | biostudies-arrayexpress

First report of vampyrellid predator-prey dynamics in a marine system.

Not available

S-EPMC6461935 | biostudies-literature

Dabrafenib plus trametinib versus dabrafenib monotherapy in patients with metastatic BRAF V600E/K-mutant melanoma: long-term survival and safety analysis of a phase 3 study.

Not available

S-EPMC5834102 | biostudies-literature

ChimeraScan: A tool for identifying chimeric transcription in sequencing data

Next Generation Sequencing technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts. Thre...

ORGANISM(S): Homo sapiens

2011-09-01 | E-GEOD-29098 | biostudies-arrayexpress

Expression of C-terminal deleted p53 isoforms in neuroblastoma.

Not available

S-EPMC1636465 | biostudies-literature

scRNAseq of Cyp11a1-expressing cells from mouse melanoma model derived tumors

Tumours induce de novo steroidogenesis in immune cells. We wanted to define the gene expression identity of intratumoural steroidogenic immune cells and compare them with the transcriptome with non-steroidogenic cells. Cyp11a1 expression is a faithful biomarker of de novo steroidogenesis (i.e. Cyp11...

ORGANISM(S): Mus musculus

2020-05-27 | E-MTAB-8509 | biostudies-arrayexpress

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