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Series GSE101406 Query DataSets for GSE101406
Status Public on Aug 24, 2017
Title Perturbational proteomic and transcriptional profiles of drug perturbations from Broad Institute LINCS Proteomic Characterization Center for Signaling and Epigenetics and Broad Institute LINCS Center for Transcriptomics (U54HG008097) (n=5,063)
Project Connectivity Map
Sample organism Homo sapiens
Experiment type Other
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 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
 
Overall design These data represent three different read-outs (phosphosignaling, chromatin modifications, and transcriptional changes) of the same 90 small-molecule perturbations in six cell lines. The duration of treatment was 3 hours for P100, 24 hours for GCP, and 6 hours for L1000. These data are available at multiple levels of processing: level 1 is fluorescence intensity (for L1000) or mass spectrometry extracted ion chromatogram traces (for P100, GCP); level 2 is gene expression or proteomic values without normalization; level 3 is normalized; and level 4 is differential (i.e., each sample is compared to all other samples on a plate).
Web link http://clue.io/proteomics
 
Citation(s) 29655704
Submission date Jul 13, 2017
Last update date Jun 04, 2018
Contact name Jacob Jaffe
E-mail jjaffe@broadinstitute.org
Organization name The Broad Institute
Lab Proteomics Platform
Street address 415 Main St.
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
GSE101406_Broad_LINCS_GCP_Level1.tar.gz 2.0 Gb (ftp)(http) TAR
GSE101406_Broad_LINCS_GCP_Level2_RPT_n1721x61.gctx.gz 348.8 Kb (ftp)(http) GCTX
GSE101406_Broad_LINCS_GCP_Level3_QCNORM_n1712x59.gctx.gz 333.4 Kb (ftp)(http) GCTX
GSE101406_Broad_LINCS_GCP_Level4_DIFF_n1712x59.gctx.gz 332.6 Kb (ftp)(http) GCTX
GSE101406_Broad_LINCS_GCP_analyte_info.txt.gz 1021 b (ftp)(http) TXT
GSE101406_Broad_LINCS_GCP_inst_info.txt.gz 14.1 Kb (ftp)(http) TXT
GSE101406_Broad_LINCS_L1000_Level1_LXB_n1667.tar.gz 1.2 Gb (ftp)(http) TAR
GSE101406_Broad_LINCS_L1000_Level2_GEX_n1667x978.gctx.gz 3.0 Mb (ftp)(http) GCTX
GSE101406_Broad_LINCS_L1000_Level3_INF_mlr12k_n1667x12328.gctx.gz 62.4 Mb (ftp)(http) GCTX
GSE101406_Broad_LINCS_L1000_Level4_ZSPCINF_mlr12k_n1667x12328.gctx.gz 64.4 Mb (ftp)(http) GCTX
GSE101406_Broad_LINCS_L1000_gene_info.txt.gz 209.2 Kb (ftp)(http) TXT
GSE101406_Broad_LINCS_L1000_inst_info.txt.gz 14.0 Kb (ftp)(http) TXT
GSE101406_Broad_LINCS_P100_Level1.tar.gz 1.6 Gb (ftp)(http) TAR
GSE101406_Broad_LINCS_P100_Level2_RPT_n1713x96.gctx.gz 486.5 Kb (ftp)(http) GCTX
GSE101406_Broad_LINCS_P100_Level3_QCNORM_n1684x96.gctx.gz 539.8 Kb (ftp)(http) GCTX
GSE101406_Broad_LINCS_P100_Level4_DIFF_n1684x96.gctx.gz 531.7 Kb (ftp)(http) GCTX
GSE101406_Broad_LINCS_P100_analyte_info.txt.gz 4.6 Kb (ftp)(http) TXT
GSE101406_Broad_LINCS_P100_inst_info.txt.gz 14.0 Kb (ftp)(http) TXT
GSE101406_Broad_LINCS_cell_info.txt.gz 494 b (ftp)(http) TXT
GSE101406_Broad_LINCS_pert_info.txt.gz 4.8 Kb (ftp)(http) TXT
GSE101406_SHA512SUMS.txt.gz 1.8 Kb (ftp)(http) TXT
Raw data is available on Series record
Processed data is available on Series record

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