Project description: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 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
Project description: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 http://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
Project description:Expression of genes highly correlated with TACSTD2 expression in breast tumors and corresponding patient-derived xenografts (PDXs) and found that 29 genes were overlapping between in 18 breast cancer samples and matching PDXs. Among these genes, TACSTD2 expression strongly correlated with expression of epithelial marker CDH1 (E-Cadherin) (r2=0.823; p<0.001). Expression of TACSTD2 was then compared to expression of CDH1 in breast cancer cell lines from The Cancer Cell Line Encyclopedia (CCLE) (N = 51) and The Library of Integrated Network-Based Cellular Signatures (LINCS) (N = 35). There was also a significant correlation between TACSTD2 and CDH1 in both CCLE (r2=0.564, p < 0.001) and LINCS (r2= 0.755; p < 0.001).
Project description: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
Project description: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 PCCSE uses two high-throughput liquid chromatography-mass spectrometry (LCMS) assays to study the proteomic changes induced by drug and genetic perturbations. P100 monitors ~100 phosphorylated peptides from cellular proteins that serve as a reduced representation of the phosphoproteome. GCP monitors ~60 modified peptides from histones (e.g., methylated, acetylated, and combinations thereof) encompassing nearly every well-studied post-translational modification on the core nucleosomal histone proteins. Closely complementing these assays is the L1000 high-throughput gene-expression assay. The files available here contain P100, GCP, and L1000 data for 90 small-molecule perturbations in six cell lines (five cancer cell lines and a neurodevelopmental cell model). These data were generated under the auspices of the NIH LINCS Program (www.lincsproject.org). Note: Related GEO projects include a large corpus of additional L1000 data, available at GSE92742. The Platform for the L1000 data is GPL20573: Broad Institute Human L1000 epsilon http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573 For questions or assistance with this dataset, please email the Connectivity Map support team at: clue@broadinstitute.org
Project description:KR-37524, known as a Urotensin-II receptor antagonist, has low usability due to its low affinity. For this reason, gene expression information was obtained by treating KR-37524 in four cell cancer cell lines to find a new target. The change in gene expression profile was measured and compared with the LINCS L1000 database and used to find a new target.
Project description:TBI was induced with lateral fluid-percussion injury in adult male rats. Genome-wide RNA-seq of the perilesional cortex, ipsilateral thalamus and dorsal hippocampus was performed at 3 months post-TBI. The data highlighted chronic transcriptional changes, particularly, in the perilesional cortex and thalamus. Genes showing a significantly altered expression both in the cortex and thalamus were submitted to the LINCS web query to identify novel pharmacotherapies to improve post-TBI outcome.
