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TranscriptomicsRNA-seq of human tissues
RNA-seq was performed of tissue samples from human individuals representing different tissues in order to study the human tissue transcriptome. This submission contains 14 samples used in the paper A proteogenomics workflow integrating discovery, curation and validation reveals human novel protein c...
ORGANISM(S): Homo sapiens 
2017-08-01 | E-MTAB-5782 | biostudies-arrayexpress
GenomicsSequencing Apoptotic DNA Breakpoints
DNA fragmentation is a well-recognized hallmark of apoptosis. However, the precise DNA sequences cleaved during apoptosis triggered by distinct mechanisms remain unclear. We used next-generation sequencing of DNA fragments generated in Actinomycin D-treated human HL-60 leukemic cells to generate a h...
ORGANISM(S): Homo sapiens 
2011-10-15 | E-GEOD-32997 | biostudies-arrayexpress
TranscriptomicsRNA-seq of A431 cell line after gefitinib treatment
RNA sequencing of A431 cell line samples before and after gefitinib treatment, at 0, 2, 6 and 24 hours, was performed in order to characterize the cell line's early and late response to this drug, and to compare against proteomics (mass spectrometry) characterization of the cell line using the same ...
ORGANISM(S): Homo sapiens 
2016-12-01 | E-MTAB-5285 | biostudies-arrayexpress
GenomicsGenome-wide mapping of Eset-binding sites and H3K9me3 state in mouse embryonic stem cells
The histone H3 lysine 9 (H3K9) methyltransferase Eset is an epigenetic regulator critical for the development of the inner cell mass (ICM). Although ICM-derived embryonic stem (ES) cells are normally unable to contribute to the trophectoderm (TE) in blastocysts, we find that depletion of Eset by shR...
ORGANISM(S): Mus musculus 
2009-11-04 | E-GEOD-17642 | biostudies-arrayexpress
GenomicsGenome-wide mapping of Nr5a2 in mouse embryonic stem cells
Nr5a2 (also known as liver receptor homolog-1, Lrh-1) has been shown to bind both the proximal enhancer and proximal promoter regions of Pou5f1 and regulate Pou5f1 in the epiblast stage of mouse embryonic development (Gu et al., 2005). Nr5a2-null embryos display a loss of Oct4 expression in the epib...
ORGANISM(S): Mus musculus 
2010-01-22 | E-GEOD-19019 | biostudies-arrayexpress
TranscriptomicsThe human skeletal muscle transcriptome assessed with RNA sequencing
The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts. Analyze of transcriptome in 24 ske...
ORGANISM(S): Homo sapiens 
2014-07-15 | E-GEOD-58608 | biostudies-arrayexpress
TranscriptomicsThe human skeletal muscle transcriptome – sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing
The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts. Analyze of transcriptome in 23 ske...
ORGANISM(S): Homo sapiens 
2014-07-15 | E-GEOD-58387 | biostudies-arrayexpress
TranscriptomicsDPN and Tamoxifen treatments of parathyroid adenoma cells
Stimulation of estrogen receptor beta in PHPT, genetic changes after 24 and 48h of treatments vs. Control Treatment of parathyroid adenomas (4 patients, 4 adenomas) with DPN 24h (4 samples), DPN 48h (4 samples), OHT 24h (4 samples), OHT 48h (4 samples), control 24h (3 samples), control 48h (4 sample...
ORGANISM(S): Homo sapiens 
2012-09-19 | E-GEOD-37211 | biostudies-arrayexpress
Proteomics,MultiomicsHiRIEFII proteomics and proteogenomics of A431 cells and five histologically normal tissues
High Resolution Isoelectric Focusing (HiRIEF) LC-MS was used to analyze samples from the human A431 cell line and also samples of histologically normal tissues. The high analytical depth afforded by HiRIEF permitted proteogenomics on these two sample sets (A431 cells and normal tissues). The A431 d...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-10-04 | MSV000083000 | MassIVE
Proteomics,MultiomicsHiRIEF deep proteomics of A431 human vulvar cancer cell line and N2A mouse neuroblastoma cell line
Here we present high resolution data from two cancer cell lines. A human cell line, A431 was treated with a drug at different time points and then fractionated into its different subcellular compartments (nuclear, organellar, soluble,whole cell). Protein extracts were trypsinized, peptides separated...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2016-07-20 | MSV000079945 | MassIVE
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