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Series GSE70138 Query DataSets for GSE70138
Status Public on Jul 15, 2015
Title L1000 Connectivity Map perturbational profiles from Broad Institute LINCS Center for Transcriptomics LINCS PHASE *II* (n=354,123; updated March 30, 2017)
Project Connectivity Map
Sample organism Homo sapiens
Experiment type Expression profiling by array
Summary The Library of Integrated Cellular Signatures (LINCS) is an NIH program which funds the generation of perturbational profiles across multiple cell and perturbation types, as well as read-outs, at a massive scale. The LINCS Center for Transcriptomics at the Broad Institute uses the L1000 high-throughput gene-expression assay to build a Connectivity Map which seeks to enable the discovery of functional connections between drugs, genes and diseases through analysis of patterns induced by common gene-expression changes.

The platform is GPL20573: Broad Institute Human L1000 epsilon

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Overall design LINCS aims to enable a functional understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The Broad Institute LINCS Center for Transcriptomics contributes to this collaborative effort by application of the Connectivity Map concept. In brief, the study design involves the generation of a compendium of transcriptional expression data from cultured human cells treated with small-molecule and genetic loss/gain of function perturbagens. These measurements are made using the L1000 high-throughput gene-expression assay that enables data generation at an unprecedented scale. 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: Level 1 (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. Level 2 (GEX) - gene expression values per 1,000 genes after deconvolution from Luminex beads. Level 3 (Q2NORM) - gene expression profiles of both directly measured landmark transcripts plus inferred genes. Normalized using invariant set scaling followed by quantile normalization. Level 4 (Z-SCORES) - signatures with differentially expressed genes computed by robust z-scores for each profile relative to control (PC relative to plate population as control; VC relative to vehicle control)
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BioProject PRJNA290347
Submission date Jun 22, 2015
Last update date Feb 14, 2018
Contact name Aravind Subramanian
Organization name The Broad Institute
Lab Connectivity Map
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA

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
GSE70138_Broad_LINCS_Level1_LXB_n345976_2017-03-06.tar.gz 223.0 Gb (ftp)(http) TAR
GSE70138_Broad_LINCS_Level2_GEX_n113012x978_2015-12-31.gct.gz 189.8 Mb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level2_GEX_n345976x978_2017-03-06.gctx.gz 637.9 Mb (ftp)(http) GCTX
GSE70138_Broad_LINCS_Level2_GEX_n78980x978_2015-06-30.gct.gz 144.4 Mb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level3_INF_mlr12k_n113012x22268_2015-12-31.gct.gz 11.1 Gb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level3_INF_mlr12k_n345976x12328_2017-03-06.gctx.gz 12.6 Gb (ftp)(http) GCTX
GSE70138_Broad_LINCS_Level3_INF_mlr12k_n78980x22268_2015-06-30.gct.gz 4.3 Gb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level4_ZSPCINF_mlr12k_n113012x22268_2015-12-31.gct.gz 14.5 Gb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level4_ZSPCINF_mlr12k_n345976x12328_2017-03-06.gctx.gz 13.1 Gb (ftp)(http) GCTX
GSE70138_Broad_LINCS_Level4_ZSPCINF_mlr12k_n78980x22268_2015-06-30.gct.gz 4.5 Gb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level4_ZSVCINF_mlr12k_n113012x22268_2015-12-31.gct.gz 14.7 Gb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level4_ZSVCINF_mlr12k_n78980x22268_2015-06-30.gct.gz 4.6 Gb (ftp)(http) GCT
GSE70138_Broad_LINCS_Level5_COMPZ_n118050x12328_2017-03-06.gctx.gz 5.0 Gb (ftp)(http) GCTX
GSE70138_Broad_LINCS_README.pdf 25.8 Kb (ftp)(http) PDF
GSE70138_Broad_LINCS_cell_info_2017-04-28.txt.gz 2.5 Kb (ftp)(http) TXT
GSE70138_Broad_LINCS_gene_info_2017-03-06.txt.gz 211.6 Kb (ftp)(http) TXT
GSE70138_Broad_LINCS_inst_info_2017-03-06.txt.gz 4.6 Mb (ftp)(http) TXT
GSE70138_Broad_LINCS_pert_info.txt.gz 81.7 Kb (ftp)(http) TXT
GSE70138_Broad_LINCS_pert_info_2017-03-06.txt.gz 80.4 Kb (ftp)(http) TXT
GSE70138_Broad_LINCS_sig_info_2017-03-06.txt.gz 1.9 Mb (ftp)(http) TXT
GSE70138_Broad_LINCS_sig_metrics_2017-03-06.txt.gz 3.0 Mb (ftp)(http) TXT
GSE70138_SHA512SUMS.txt.gz 1.0 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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