NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE92743 Query DataSets for GSE92743
Status Public on Mar 03, 2017
Title Broad Institute L1000 Connectivity Map and RNAseq gene expression profiles on tissue samples from the GTEx project
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 profile a range of cellular models and perturbations of cellular state. These data relate to using RNA-Seq datasets from the GTEx consortium (http://www.gtexportal.org/) to validate the L1000 assay and to improve the statistical model used in imputing the transcriptome.

The Platform is GPL20573: Broad Institute Human L1000 epsilon
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573

For questions or assistance with this dataset, please email the CMap support team at: clue@broadinstitute.org
 
Overall design The Genotype Tissue Expression (GTEx) project aims to find associations between genomic features and gene expression levels. As part of this project, aliquots of mRNA obtained from 3,176 patient-derived samples from 30 tissue types were profiled on two contemporary gene expression platforms; RNAseq and L1000, a high-throughput gene-expression assay that enables data generation at an unprecedented scale. In L1000, the data are processed through a computational system that converts raw fluorescence intensities into normalized expression profiles generating level 3 (Q2NORM) - gene expression profiles of both directly measured landmark transcripts plus inferred genes. Normalization is done using invariant set scaling followed by quantile normalization. The RNAseq data were collected using Illumina TrueSeq RNA sequencing and converted into reads per kilobase-million (RPKM) units. These RPKM data and underlying read count files are available via the GTEx portal (http://www.gtexportal.org/home/datasets). In this series, the RPKM data were also log2-scaled and quantile normalized as a cohort.
Web link https://clue.io
 
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
GSE92743_Broad_Affymetrix_training_Level3_Q2NORM_n100000x12320.gctx.gz 2.2 Gb (ftp)(http) GCTX
GSE92743_Broad_GTEx_L1000_Holdout_Level3_Q2NORM_n1000x12320.gctx.gz 37.7 Mb (ftp)(http) GCTX
GSE92743_Broad_GTEx_L1000_Level3_Q2NORM_n3176x12320.gctx.gz 120.0 Mb (ftp)(http) GCTX
GSE92743_Broad_GTEx_L1000_NotUsed_Level3_Q2NORM_n1526x12320.gctx.gz 57.6 Mb (ftp)(http) GCTX
GSE92743_Broad_GTEx_L1000_Test_Level3_Q2NORM_n650x12320.gctx.gz 24.5 Mb (ftp)(http) GCTX
GSE92743_Broad_GTEx_RNAseq_Log2RPKM_q2norm_n3176x12320.gctx.gz 110.3 Mb (ftp)(http) GCTX
GSE92743_Broad_GTEx_gene_info.txt.gz 212.6 Kb (ftp)(http) TXT
GSE92743_Broad_GTEx_inst_info.txt.gz 42.0 Kb (ftp)(http) TXT
GSE92743_Broad_OLS_WEIGHTS_n979x11350.gctx.gz 20.3 Mb (ftp)(http) GCTX
GSE92743_Broad_README.pdf 25.8 Kb (ftp)(http) PDF
GSE92743_SHA512SUMS.txt.gz 939 b (ftp)(http) TXT
Raw data is available on Series record
Processed data is available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap