Broad Institute L1000 Connectivity Map and RNAseq gene expression profiles on tissue samples from the GTEx project

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: [e-mail] 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.