Gerber B B - OmicsDI

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Unknown (669)
Transcriptomics (65)
Proteomics (36)
Metabolomics (6)
Genomics (3)
Other (1)

Organisms

Saccharomyces cerevisiae (35)
Homo sapiens (28)
Mus musculus (13)
Caenorhabditis elegans (7)
Drosophila melanogaster (4)
Trypanosoma brucei (4)
Pseudomonas aeruginosa PAO1 (1)
Bos taurus (1)
Arabidopsis thaliana (1)
Aspergillus fumigatus (1)
Dermatophagoides pteronyssinus (1)
Aspergillus niger (1)
Clostridium botulinum F str. Langeland (1)
Clostridium botulinum str. LANGELAN F (1)
Geobacillus kaustophilus HTA426 (1)
Lasiodiplodia theobromae (1)
Macaca mulatta (1)
Murine hepatitis virus strain A59 (1)
Mycobacterium tuberculosis GM 1503 (1)
Mycoplasmoides pneumoniae M129 (1)
Oryctolagus cuniculus (1)
Pasteurella multocida subsp. multocida str. Pm70 (1)
Rattus norvegicus (1)
Schizosaccharomyces pombe (1)

Repository

biostudies-arrayexpress (68)
pride (33)
MetaboLights (6)
PanoramaPublic (2)
GPMDB (1)
MassIVE (1)

Tissue

Cell culture (11)
Fibroblast (9)
Brain (2)
Epithelial cell (2)
Haploid cell (1)
Hepatocyte (1)
Kidney (1)
Liver (1)
Mycelium (1)
Pancreas (1)
Skeletal muscle (1)

Disease

Disease free (2)
Not Available (1)
Cardiovascular system disease (1)
Hepatocellular carcinoma (1)
Keratitis (1)
Pancreatic ductal adenocarcinoma (1)
Pneumonia (1)
Tinea unguium (1)
Wounds and Injuries (1)

Technology Type

Mass Spectrometry (33)
Shotgun proteomics (15)
Gel-based experiment (10)
Affinity purification coupled with mass spectrometry proteomics (8)
Mass spectrometry (6)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
Data-dependent acquisition (3)
Bottom-up proteomics (2)
Data-independent acquisition (1)
SRM/MRM (1)

Instrument Platform

Illumina NovaSeq 6000 (6)
Liquid Chromatography MS - positive - reverse phase (3)
Liquid Chromatography MS - negative - reverse phase (2)
Illumina Genome Analyzer IIx (1)
Axon GenePix 4000B scanning hardware (1)
Vortex (1)
Instrument (1)
Orbitrap Fusion (1)
Gas Chromatography MS - positive (1)
LCT Premier XE (Waters) (1)
Liquid Chromatography MS - negative - HILIC (1)
Liquid Chromatography MS - positive - HILIC (1)
SYNAPT G2 HDMS (Waters) (1)
LCQ Deca XP Plus (1)

Publication Date

2010 (17)
2021 (13)
2012 (10)
2013 (8)
2006 (7)
2016 (6)
2024 (5)
2019 (5)
2015 (5)
2023 (5)
2005 (4)
2020 (4)
2026 (4)
2025 (3)
2011 (3)
2008 (3)
2018 (3)
2017 (2)
2014 (1)
2007 (1)

CHEBI ID

CHEBI:77131 (3)
CHEBI:116314 (2)
CHEBI:15428 (2)
CHEBI:15584 (2)
CHEBI:15741 (2)
CHEBI:16015 (2)
CHEBI:16057 (2)
CHEBI:16414 (2)
CHEBI:16643 (2)
CHEBI:16857 (2)
CHEBI:17053 (2)
CHEBI:17203 (2)
CHEBI:17497 (2)
CHEBI:17754 (2)
CHEBI:17858 (2)
CHEBI:18012 (2)
CHEBI:18050 (2)
CHEBI:18211 (2)
CHEBI:18292 (2)
CHEBI:18344 (2)
CHEBI:22990 (2)
CHEBI:28238 (2)
CHEBI:28842 (2)
CHEBI:30797 (2)
CHEBI:30915 (2)
CHEBI:37024 (2)
CHEBI:4676 (2)
CHEBI:68883 (2)
CHEBI:71169 (2)
CHEBI:83058 (2)

Metabolite Name

Citramalic acid (2)
D-Glucose (2)
Fumaric acid (2)
Glycerol (2)
Glycine (2)
Glycolic acid (2)
L-Aspartic acid (2)
L-Glutamine (2)
L-Malic acid (2)
L-Proline (2)
L-Threonine (2)
L-Valine (2)
Oxoglutaric acid (2)
Pyroglutamic acid (2)
Sinapic acid (2)
Stearic acid (2)
(+)-artemisinin (1)
(+)-haematoxylin (1)
(+)-neoisodihydrocarveol (1)
(+-)N-(2-fluro-ethyl)-2,16-dimethyl-5Z,8Z,11Z,14Z-docosatetraenoyl amine (1)
(-)-Ngaione (1)
(-)-Obtusadiene (1)
(-)-cis-carveol (1)
(1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene (1)
(20R)-20-hydroxypregn-4-en-3-one (1)
(22E)-3beta-hydroxy-5alpha-chola-7,22-dien-24-oic acid (1)
(2E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (1)
(3E)-3-nonen-2-one (1)
(3R,9E)-heptadeca-1,9-diene-4,6-diyn-3-ol (1)
(4E,6E,d14:2) sphingosine (1)

Modification

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

Study type

Transcription profiling by array (33)
Other (10)
Unknown experiment type (7)
ChIP-chip by array (4)
RNA-seq of coding RNA from single cells (4)
ChIP-seq (3)
RIP-chip by array (2)
Cell line - Single-cell sequencing (1)
Cell line - High-throughput sequencing (1)
CLIP-seq (1)
Comparative genomic hybridization by array (1)
RNA-seq of coding RNA (1)

Release Date

2022 (85)
2025 (68)
2023 (66)
2024 (65)
2021 (65)
2020 (50)
2019 (45)
2018 (40)
2012 (36)
2011 (30)
2017 (29)
2016 (26)
2013 (25)
2014 (23)
2010 (21)
2015 (17)
2026 (13)
2006 (9)
2008 (6)
2007 (6)
2005 (5)
2009 (5)
2004 (1)
2001 (1)

Lab affiliation

Research Group Mitochondrial Disorders, Institute of Human Genetics, Technische Universität München, München, Germany (5)
Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Germany (2)
Biozentrum Basel, University of Basel, Basel, Switzerland (1)
CSIR- Institute of Microbial Technology, Chandigarh (1)
Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, Barcelona 08003, Spain. (1)
Department of Plastic and Burn Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an 710038, China (1)
Department of Psychiatry, Yale University School of Medicine, New Haven, CT (1)
Departments of Genetics and Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA (1)
Dept. of Microbial Sciences School of Biosciences and Medicine Faculty of Health and Medical Sciences University of Surrey Stag Hill Campus 19 AX 01 Guildford, GU2 7XH U.K. (1)
Dept. of Microbial and Cellular Sciences Faculty of Health and Medical Sciences University of Surrey Stag Hill Campus 19 AX 01 Guildford, GU2 7XH U.K. (1)
Emory University School of Medicine Department of Pharmacology (1)
Fred Hutch Cancer Center, Human Biology Division (1)
Harvard Medical School (1)
Institute of Cell Biology, University of Bern (1)
Institute of Cell Biology, University of Berne, Switzerland (1)
Institute of Virology and Immunology IVI, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland (1)
Johns Hopkins School of Medicine, Division of Cardiology (1)
PUCRS and UCSD - Pontifícia Universidade Católica do Rio Grande do Sul; and University of California at San Diego. Dept: Cell and Molecular Biology; and Department of Surgery (1)
Proteomics Core Facility, University of Gothenburg (1)
Research Group of Mitochondrial Disorders, Institute of Human Genetics, Technische Universität München, München (1)
Research Group of Mitochondrial Disorders, Institute of Human Genetics, Technische Universität München, München, Germany (1)
Sequence database group (1)
Sorbonne Universités - UPMC Univ Paris 6 - UMR7238, Laboratoire de biologie computationnelle et quantitative, F-75006 PARIS, France (1)
T.N.C. Ramya Principal Scientist CSIR-Institute of Microbial Technology Sector 39-A, Chandigarh 160036 INDIA Tel: 91-172-6665243; E-mail: ramya@imtech.res.in (1)
UNIVERSITY OF SURREY (1)
University of California, San Diego Proteomics Mass Spectrometry Depertment (1)
University of Nottingham, School of Life Sciences (1)
University of Surrey (1)

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Khd1p associated mRNAs

RNA-coimmunopurifications with TAP-tagged Khd1 protein from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control (Gerber et al., 2004). Cells were grown to midlog phase in rich media and harvested by centrifugation. TAP-tagged Khd1 was affinity purified from cell-free extracts with...

ORGANISM(S): Saccharomyces cerevisiae

2010-06-20 | E-GEOD-10279 | biostudies-arrayexpress

Puf proteins, RNA co-immunopurification

RNA-coimmunopurifications with TAP-tagged Puf proteins from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control. Cells were grown to midlog phase and harvested by centrifugation. TAP-tagged Puf proteins were affinity purified from cell-free extracts with IgG sepharose and eluted ...

ORGANISM(S): Saccharomyces cerevisiae

2006-01-03 | E-GEOD-3968 | biostudies-arrayexpress

Chromatin immunoprecipitation with TAP-tagged Puf proteins from Saccharomyces cereviseae

ORGANISM(S): Saccharomyces cerevisiae

2005-11-01 | E-SMDB-2622 | biostudies-arrayexpress

Shg1p associated RNAs

RNA co-immunopurification with TAP-tagged Shg1p (a component of the Set1 histone methyltransferase complex, SET1C) from Saccharomyces cerevisiae. An untagged (BY4741) served as a control (Gerber et al. 2004). Cells were grown to mid-log phase in rich media and harvested by centrifugation. TAP-tagged...

ORGANISM(S): Saccharomyces cerevisiae

2010-06-24 | E-GEOD-15247 | biostudies-arrayexpress

Circulating clonotypic B cells in classic Hodgkin lymphoma.

Not available

S-EPMC2700327 | biostudies-literature

RBP40_arrays

In this study, we systematically identified the RNAs associated with a selective sample of 40 of ~600 yeast RNA-binding proteins (RBPs). To identify RNAs associated with each putative RBP, C-terminal tandem affinity purification (TAP)-tagged proteins, expressed under control of their native promoter...

ORGANISM(S): Saccharomyces cerevisiae

2010-06-25 | E-GEOD-13135 | biostudies-arrayexpress

Slf1p and Sro9p affinity isolations

To identify RNAs specifically associated with Slf1p and Sro9p, cells expressing TAP-tagged Slf1, Sro9 or Fpr1 (negative control) were grown to mid-log phase in synthetic complete medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al. 20...

ORGANISM(S): Saccharomyces cerevisiae

2012-02-08 | E-GEOD-27310 | biostudies-arrayexpress

Pom1-AS quantitative phosphoproteomics

Complex phosphorylation-dependent signaling networks underlie the coordination of cellular growth and division. In the fission yeast S. pombe, the DYRK family protein kinase regulates cell cycle progression through the mitotic inducer Cdr2, and controls cell polarity through unknown targets. Here, w...

ORGANISM(S): Schizosaccharomyces pombe

2015-03-09 | PXD001649 | Pride

RNA-affinity isolations 13 RBPs

To identify RNAs specifically associated with potential RBPs, yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al...

ORGANISM(S): Saccharomyces cerevisiae

2010-12-06 | E-GEOD-21864 | biostudies-arrayexpress

Peanut oral immunotherapy transiently expands circulating Ara h 2-specific B cells with a homologous repertoire in unrelated subjects.

Not available

S-EPMC4494892 | biostudies-literature

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