Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of A431 cell line after gefitinib treatment

ABSTRACT: 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 setup. These data were used in Branca et al., HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics., Nat Methods. 2014 Jan;11(1):59-62 (doi: 10.1038/nmeth.2732).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Rui Branca 

PROVIDER: E-MTAB-5285 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Branca Rui M M RM   Orre Lukas M LM   Johansson Henrik J HJ   Granholm Viktor V   Huss Mikael M   Pérez-Bercoff Åsa Å   Forshed Jenny J   Käll Lukas L   Lehtiö Janne J  

Nature methods 20131117 1

We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectivel  ...[more]

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