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Series GSE106127 Query DataSets for GSE106127
Status Public on Oct 30, 2017
Title Datasets Used in Evaluation Of RNAi And CRISPR Technologies By Large Scale Gene Expression Profiling In The Connectivity Map
Project Connectivity Map
Sample organism Homo sapiens
Experiment type Expression profiling by array
Summary This GEO Series contains datasets used in the paper "Evaluation Of RNAi And CRISPR Technologies By Large Scale Gene Expression Profiling In The Connectivity Map". The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes. Although RNAi has revolutionized loss of function genetic experiments, it has been difficult to systematically assess the prevalence and consequences of off-target effects. The Connectivity Map (CMAP) represents an unprecedented resource to study the gene expression consequences of expressing short hairpin RNAs (shRNAs). Analysis of signatures for over 13,000 shRNAs applied in 9 cell lines revealed that miRNA-like off-target effects of RNAi are far stronger and more pervasive than generally appreciated. We show that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a Consensus Gene Signature (CGS). In addition, we compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 sgRNAs in 6 cells lines, and show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off-target effects. These results will help guide the proper use and analysis of loss-of-function reagents for the determination of gene function. Note: Related GEO projects include a large corpus of additional L1000 data, available at GSE92742.

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 The datasets in this Series were generated as part of the LINCS project, which 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 provided here include Levels 4 and 5, as well as additional data described in the README: 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. For more data levels and their descriptions, please consult GSE92742.
Web link
Citation(s) 29190685
Submission date Oct 24, 2017
Last update date Sep 08, 2021
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
GSE106127_CGS_PRIME_meta.txt.gz 2.1 Mb (ftp)(http) TXT
GSE106127_CGS_PRIME_n33839x978.gctx.gz 135.2 Mb (ftp)(http) GCTX
GSE106127_CGS_meta.txt.gz 2.1 Mb (ftp)(http) TXT
GSE106127_CGS_n33839x978.gctx.gz 135.0 Mb (ftp)(http) GCTX
GSE106127_README.pdf.gz 24.8 Kb (ftp)(http) PDF
GSE106127_SHA512SUMS.txt.gz 1.2 Kb (ftp)(http) TXT
GSE106127_gene_info.txt.gz 16.8 Kb (ftp)(http) TXT
GSE106127_inst_info.txt.gz 2.8 Mb (ftp)(http) TXT
GSE106127_level_4_PRIME_zspc_n341336x978.gctx.gz 1.3 Gb (ftp)(http) GCTX
GSE106127_level_4_zspc_n341336x978.gctx.gz 1.0 Gb (ftp)(http) GCTX
GSE106127_level_5_PRIME_modz_n119013x978.gctx.gz 476.8 Mb (ftp)(http) GCTX
GSE106127_level_5_modz_n119013x978.gctx.gz 463.8 Mb (ftp)(http) GCTX
GSE106127_pc_coeff_global_n978x978.gctx.gz 3.9 Mb (ftp)(http) GCTX
GSE106127_sig_info.txt.gz 3.0 Mb (ftp)(http) TXT
GSE106127_sig_metrics.txt.gz 5.3 Mb (ftp)(http) TXT
Processed data are available on Series record

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