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Series GSE83744 Query DataSets for GSE83744
Status Public on Jun 28, 2016
Title High-throughput phenotyping of lung cancer somatic mutations [main experiment]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas using L1000 high-throughput gene-expression assays followed by expression-based variant impact phenotyping (eVIP), a method that uses gene expression changes to distinguish impactful from netural somatic mutations. This series represents the main experiment of the study where 8 replicates of wild-type and mutant ORFs are introduced into A549 cell lines.
 
Overall design An ORF library containing wild-type and mutated versions of genes found to be mutated in lung cancer are introduced in A549 cell lines and measurements are made using the L1000 high-throughput gene-expression assay. These are done with 8 replicate experiemnts. The data are processed through a computational system, that converts raw fluorescence intensities into differential gene expression signatures. The data at each stage of the pre-processing are available: (LXB) - raw, unprocessed flow cytometry data from Luminex scanners. One LXB file is generated for each well of a 384-well plate, and each file contains a fluorescence intensity value for every observed analyte in the well. (Q2NORM) - gene expression profiles of directly measured landmark transcripts. Normalized using invariant set scaling followed by quantile normalization. (Z-SCORES) - signatures with differentially expressed genes computed by robust z-scores for each profile relative to control (relative to plate population as control)
 
Contributor(s) Brooks AN, Berger AH, Wu X, Meyerson M, Boehm JS
Citation(s) 27478040
Submission date Jun 27, 2016
Last update date Sep 27, 2016
Contact name Jesse S. Boehm
Organization name Broad Institute
Street address 415 Main Street
City Cambridge
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL22085 Broad Institute Human L1000 landmark
Samples (3738)
GSM2214682 ACAT2_WT_V5_rep1_TA.OE014_A549_96H_X1_B19:A03
GSM2214683 EBNA1BP2_WT_V5_rep1_TA.OE014_A549_96H_X1_B19:A04
GSM2214684 BFP_rep1_TA.OE014_A549_96H_X1_B19:A05
Relations
BioProject PRJNA326921

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83744_RAW.tar 2.6 Gb (http)(custom) TAR (of LXB)
GSE83744_lung_cancer_mutations_main_8rep_z_scores.txt.gz 7.9 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Processed data is available on Series record

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