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Series GSE92742 Query DataSets for GSE92742
Status Public on Mar 03, 2017
Title L1000 Connectivity Map perturbational profiles from Broad Institute LINCS Center for Transcriptomics LINCS Pilot PHASE I (n=1,319,138; updated March 03, 2017)
Project Connectivity Map
Sample organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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. These files represent L1000 data generated during the LINCS Pilot Phase (2012-2015), as well as profiles generated for more specific purposes, such as assay development and validation projects or testing custom compounds or non-standard cell lines (not part of the core LINCS cell lines). Note: Related GEO projects include (a) Additional L1000 and RNA-Seq data used to validate the assay and improve the inference model, available at GSE92743 (b) The LINCS “production phase” (also termed Phase II, 2015-2020) which is generating an additional cohort of L1000 data, available at GSE70138.

The Platform is GPL20573: Broad Institute Human L1000 epsilon

For questions or assistance with this dataset, please email the CMap support team at:
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). Level 5 (SIG) consists of the replicates, usually 3 per treatment, aggregated into a single differential expression vector derived from the weighted averages of the individual replicates.

Please note that a description of the latest file, and a table listing the contents of the 'Broad_LINCS_auxiliary_datasets.tar.gz' file are updated in the following document;
Web link
Citation(s) 29195078
Submission date Dec 22, 2016
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
GSE92742_Broad_LINCS_Level1_LXB_n1403502.tar.gz 1.2 Tb (ftp)(http) TAR
GSE92742_Broad_LINCS_Level2_GEX_delta_n49216x978.gctx.gz 98.9 Mb (ftp)(http) GCTX
GSE92742_Broad_LINCS_Level2_GEX_epsilon_n1269922x978.gctx.gz 2.3 Gb (ftp)(http) GCTX
GSE92742_Broad_LINCS_Level3_INF_mlr12k_n1319138x12328.gctx.gz 48.8 Gb (ftp)(http) GCTX
GSE92742_Broad_LINCS_Level4_ZSPCINF_mlr12k_n1319138x12328.gctx.gz 49.6 Gb (ftp)(http) GCTX
GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx.gz 19.9 Gb (ftp)(http) GCTX
GSE92742_Broad_LINCS_README.pdf 25.8 Kb (ftp)(http) PDF
GSE92742_Broad_LINCS_auxiliary_datasets.tar.gz 1.6 Gb (ftp)(http) TAR
GSE92742_Broad_LINCS_cell_info.txt.gz 2.5 Kb (ftp)(http) TXT
GSE92742_Broad_LINCS_gene_info.txt.gz 211.6 Kb (ftp)(http) TXT
GSE92742_Broad_LINCS_gene_info_delta_landmark.txt.gz 18.3 Kb (ftp)(http) TXT
GSE92742_Broad_LINCS_inst_info.txt.gz 11.5 Mb (ftp)(http) TXT
GSE92742_Broad_LINCS_pert_info.txt.gz 1.1 Mb (ftp)(http) TXT
GSE92742_Broad_LINCS_pert_metrics.txt.gz 908.9 Kb (ftp)(http) TXT
GSE92742_Broad_LINCS_sig_info.txt.gz 10.6 Mb (ftp)(http) TXT
GSE92742_Broad_LINCS_sig_metrics.txt.gz 11.9 Mb (ftp)(http) TXT
GSE92742_SHA512SUMS.txt.gz 1.4 Kb (ftp)(http) TXT
Raw data is available on Series record
Processed data is available on Series record

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