Public Datasets
RNA-seq
54 mRNA-seq samples from baseline, unperturbed breast cancer cell lines were profiled using Illumina Genome Analyzer IIx to identify patterns of gene expression associated with subtype and response to therapeutic compounds. Data were generated by Microenvironment Perturbagen (MEP) LINCS Center at Oregon Health and Science University.
Daemen A, Griffith OL, Heiser LM, Wang NJ et al. Modeling precision treatment of breast cancer. Genome Biol 2013;14(10):R110.
source=EDS-1014, LINCS ID=EDS-1014
P100
141 samples from 3 cell lines under ~45 perturbational conditions were profiled by mass spectrometry-based proteomics assay to detect and quantify 90 phosphopeptide probes. Data were generated by LINCS Proteomic Characterization Center for Signaling and Epigenetics at Broad Institue.
source=LDG-1193, LINCS ID=LDG-1193
RPPA
52 untreated breast cancer cell samples were profiled by reverse protein lysate array (RPPA) in Gordon Mills lab at MD Anderson to quantitatively measure protein abundance. Data were generated by Microenvironment Perturbagen (MEP) LINCS Center at Oregon Health and Science University.
Daemen A, Griffith OL, Heiser LM, Wang NJ et al. Modeling precision treatment of breast cancer. Genome Biol 2013;14(10):R110.
source=EDS-1013, LINCS ID=EDS-1013
RNA-seq
35 RNA-seq samples from human brain cell types were profiled to develope a network of unique cell signatures relevant to two types of motor neuron diseases namely Amyotrophic lateral sclerosis (ALS) and Spinal muscular atrophy (SMA). Data were generated by NeuroLINCS Center at the University of California, Irvine
source=LDG-1232, LINCS ID=LDG-1232
GCP
473 samples from 5 cell lines perturbed by 32 neurodev compounds for 24 hours were profiled by mass spectrometry-based proteomics assay to detect and quantify 59 histone proteins. Data were generated by LINCS Proteomic Characterization Center for Signaling and Epigenetics at Broad Institue.
source=LDG-1230, LINCS ID=LDG-1230
RNA-seq
183 RNA-seq samples from human cell lines were profiled to develop cellular signatures for drug-induced toxicity caused by FDA approved drugs and toxicity mitigation by coadministration of other drugs. Data were generated by Drug Toxicity Signature Generation Center at Icahn School of Medicine at Mount Sinai
source=LDG-1231, LINCS ID=LDG-1231
RNA-seq
378 RNA-seq samples from human cell lines were profiled to develop cellular signatures for drug-induced toxicity caused by FDA approved drugs and toxicity mitigation by coadministration of other drugs. Data were generated by Drug Toxicity Signature Generation Center at Icahn School of Medicine at Mount Sinai
source=LDG-1233, LINCS ID=LDG-1233
P100
465 samples from 5 cell lines perturbed by 32 epigenetic compounds for 3 hours were profiled by mass spectrometry-based proteomics assay to detect and quantify 96 phosphopeptide probes. Data were generated by LINCS Proteomic Characterization Center for Signaling and Epigenetics at Broad Institue.
source=LDG-1228, LINCS ID=LDG-1228
P100
373 samples from 2 cell lines perturbed by 32 kinase inhibitors for 3 hours were profiled by mass spectrometry-based proteomics assay to detect and quantify 94 phosphopeptide probes. Data were generated by LINCS Proteomic Characterization Center for Signaling and Epigenetics at Broad Institue.
source=LDG-1255, LINCS ID=LDG-1255
GCP
287 samples from 3 cell lines perturbed by 32 kinase inhibitors for 24 hours were profiled by mass spectrometry-based proteomics assay to detect and quantify 53 histone proteins. Data were generated by LINCS Proteomic Characterization Center for Signaling and Epigenetics at Broad Institue.
source=LDG-1256, LINCS ID=LDG-1256
L1000
216,105 transcriptional signatures of cellular perturbations constructed using the LINCS pilot phase L1000. The chemical perturbagen and individual shRNA signatures are created by aggregating (ie averaging) Level 4 data for biological replicates as defined by the signatures metadata. Only signatures designated to be reproducible and self-connected ("gold") by the Broad institute are represented. Consensus Gene Signatures (CGS) are constructed by further aggregating signatures of individual shRNA perturbations. Signatures are based only on the 978 Landmark Genes measured directly by the L1000 assay.
source=LDG-1188, LINCS ID=LDG-1188
Find GEO Dataset for a LINCS Chemical Perturbagen
Search Term
GEO GSE/GDS ID (e.g. GDS2300), MeSH heading (e.g. Milrinone), LINCS chemical perturbagen ID (e.g. BRD-K67080878-001-11-3, LSM-3493), PubChem compound ID (e.g. 4197).
Matching Chemicals and GEO Terms
Datasets generated by LINCS data and signature generation centers
mRNA-seq data generated by The Cancer Genome Atlas project
Genome-scale datasets related to breast cancer
GDS
Gene Expression Omnibus Datasets (GDS)
Cancer related genomics datasets
Uncategorized useful gene expression datasets
Genome-scale datasets related to prostate cancer
A collection of toxicogenomics datasets
Juvenile Rheumatoid Arthritis (JRA)
Genomics datasets assessing health effects of Bisphenol A
Genomics datasets related to stem cells and development
Gene expression microarray datasets generated by the BCERC project (mostly private)
Clinical and Translational Science Awards (CTSA) program