Project description:LC-MS analysis of 18 OGE fractions optained from normally grown U2OS cell lysates. The generation of mathematical models of biological processes, the simulation of these processes under different conditions, and the comparison and integration of multiple data sets are explicit goals of systems biology that require the knowledge of the absolute quantity of the system’s components. To date, systematic estimates of cellular protein concentrations have been exceptionally scarce. Here, we provide a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis. We show that these human cultured cells express at least 10000 proteins and that the quantified proteins span a concentration range of seven orders of magnitude up to 20000000 copies per cell. We discuss how protein abundance is linked to function and evolution. Regarding the bioinformatics pipeline employed: the acquired raw files were converted to the centroid mxxml and mgf-format using MassMatrix mass spectrometric data file conversion tools (version 3.9, http://www.massmatrix.org) and searched using MASCOT (version 2.4) against a decoy database of the predicted proteome from homo sapiens extracted from the UniProt/SwissProt database (downloaded on 16/05/2012) and including known contaminants such as keratins/trypsin. The search criteria were set as follows: full tryptic specificity was required (cleavage after lysine or arginine residues); 3 missed cleavages were allowed; carbamidomethylation (C) was set as fixed modification; oxidation (M) as variable modification. The mass tolerance was set to 15 ppm for precursor ions and 0.5 Da for fragment ions.

2013-02-22 | PXD000157 | Pride

FOXJ3 ChIP-seq in a U2OS stable cell line

Project description:Chromatin immuno-precipitation using anti-Flag (Sigma) antibodies in a U2OS stable cell line. Paired-end R1 and R2 reads are provided, but the processed (mapped) reads are from a single-end (R1 read only) mapping.

2015-12-03 | E-MTAB-3687 | biostudies-arrayexpress

Homo sapiens strain:U2OS

Project description:Homo sapiens strain:U2OS Transcriptome or Gene expression

| PRJNA251691 | ENA

Homo sapiens strain:U2OS

Project description:Homo sapiens strain:U2OS Transcriptome or Gene expression

| PRJNA578349 | ENA

Expression data from C33-A cell line

Project description:C33-A is a Homo sapiens cervix carcinoma cell line. In this experiment we determine the level of gene expression under exponentially growing conditions. The final goal of the experiment is to correlate other epigenetic characteristics from other experiments with gene expression levels. C33-A cells from three independent exponentially growing cultures were recovered and processed for RNA extraction and hybridization on Affymetrix microarrays

2013-07-17 | E-GEOD-48926 | biostudies-arrayexpress

Homo sapiens strain:U2OS cells

Project description:Homo sapiens strain:U2OS cells Targeted Locus (Loci)

| PRJNA244309 | ENA