Next Generation Sequencing of normal human intestinal epithelial cell lines, CRC cell lines and CRC cell lines with hypoxia treatment
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE163868 | GEO | 2023/12/25
REPOSITORIES: GEO
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Project description:Next Generation Sequencing of normal human intestinal epithelial cell lines, CRC cell lines and CRC cell lines with hypoxia treatment
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Project description:There is a need for robust phosphopeptide enrichment methods to allow signaling network analysis in cancer cell lines and tissues with minimal fractionation. With recent instrument developments thousands of unique phosphopeptides can be detected by single-shot LC-MS/MS. However, successful phosphoproteomics experiments still rely on efficient phosphopeptide enrichment from a tryptic digest prior to LC-MS/MS analysis. Here we describe a performance assessment of HAMMOC (hydroxyl acid modified metal affinity chromatography) (Sugiyama MCP2007, Kyono, JPR 2008) combined with single shot label-free quantitation at 500 µg peptide input level. We apply the method to profile the baseline phosphorylation landscape of a panel of 8 colorectal cancer (CRC) cell lines. These CRC cell lines represent the 3 CRC subtypes (CCS1, CCS2 and CCS3) as reported by large-scale transcriptome analysis. We report an analysis of the phosphoprotein network and processes enriched in the cell lines representing the poor prognosis CCS3 subtype.
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