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MetabolomicsA multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that capt...

2020-02-14 | MTBLS1320 | MetaboLights
ProteomicsIn-depth proteome analysis of Hela cell culture conditioned media containing fetal bovine serum.
We performed DIA-MS based proteomic analysis of Hela cells conditioned media containing fetal bovine serum by albumin (Alb)-depletion and non-depletion. In addition, we attempted to enrich secreted proteins by reducing the volume of culture medium (10mL, 5mL and 2mL). The supernatants of each cultur...
ORGANISM(S): Homo Sapiens (human) 
2022-02-22 | PXD024272 | JPOST Repository
TranscriptomicsA modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
We examine the use of high-throughput sequencing on binding sites recovered using a bacterial one-hybrid (B1H) system and find that improved models of transcription factor (TF) binding specificity can be obtained compared to standard methods of sequencing a small subset of the selected clones. We ca...
ORGANISM(S): synthetic construct 
2011-04-28 | E-GEOD-26767 | biostudies-arrayexpress
GenomicsChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by SOLiD
We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation. Examination of Yfl052 trancription factor in HA-tagged and wt cells...
ORGANISM(S): Saccharomyces cerevisiae 
2014-07-24 | E-GEOD-57901 | biostudies-arrayexpress
ProteomicsUn-conditioned commercial embryo culture media contain a large variety of non-declared proteins: a comprehensive proteomics analysis
Study question: Which non-declared proteins (proteins not listed on the composition list of the product data sheet) are present in unconditioned commercial embryo culture media? Summary answer: A total of 110 non-declared proteins were identified in unconditioned media and between 6 and 8 of these ...
ORGANISM(S): Homo sapiens (Human) 
2014-09-01 | PXD001174 | Pride
Embryo Proteomics Culture media Ivf Secretome Lc-ms/ms 
MetabolomicsEx-Vivo Equine Cartilage Explant Osteoarthritis Model - A Metabolomics and Proteomics Study
Osteoarthritis (OA) is an age-related degenerative musculoskeletal disease characterised by loss of articular cartilage, synovitis, abnormal bone proliferation and subchondral bone sclerosis. Underlying OA pathogenesis is yet to be fully elucidated with no OA specific biomarkers in clinical use. Ex-...
2020-09-30 | MTBLS1495 | MetaboLights
GenomicsLigand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating Retinoic Acid Receptor (RAR)-mediated transcription. RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the ret...
ORGANISM(S): Mus musculus 
2010-12-10 | E-GEOD-19409 | biostudies-arrayexpress
GenomicsChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by Illumina
We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation. Examination of Yfl052 trancription factor in HA-tagged and wt cells...
ORGANISM(S): Saccharomyces cerevisiae 
2014-07-24 | E-GEOD-57900 | biostudies-arrayexpress
TranscriptomicsGene expression profiling of human mammary artery media during aging
Our goal was to better understand the genes and pathways implicated during arterial media aging. We therefore compared the gene expression profile of human mammary artery media between Young (<60, 8 patients) and old (>75, 7 patients) patients. The microarray data, generated using the Illumina sentr...
ORGANISM(S): Homo sapiens 
2010-12-07 | E-GEOD-16487 | biostudies-arrayexpress
TranscriptomicsGenome-Wide STAT5 binding sites in Kit225 leukemia cells
In order to systematically map STAT5 genomic binding sites and IL-2 mediated gene expression changes we mapped STAT5 binding sites using chip-on-ChIP in IL-2 dependent Kit225 cells that were either left un-stimulated or stimulated with IL-2 for 30 minutes. Using MAT analysis we identified 1581 STAT5...
ORGANISM(S): Homo sapiens 
2013-03-21 | E-GEOD-40619 | biostudies-arrayexpress
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