Connectivity Map (CMAP O2) gene expression

{"name":"probeMap/Illumina1M.hg18.probeMap","assembly":"hg18","dbxref":"Illumina web site https://icom.illumina.com/download/summary/shya74zLlECtbg_93evrOQ Human1M-Duov3_B-H_MappingInformation.zip","type":"probeMap","version":"2012-06-26","idtype":"probe","label":"Illumina Human1M-Duo array (hg18) e.g. rs999721"}

{"owner":"literature","longTitle":"GBM CGH (Parsons et al. 2008)","cohort":"GBM (Parsons 2008)","url":"http://www.ncbi.nlm.nih.gov/pubmed/18772396","probeMap":"probeMap/Illumina1M.hg18.probeMap","dataSubType":"copy number","citation":"Science. 2008 Sep 26;321(5897):1807-12. Epub 2008 Sep 4.","label":"Parsons GBM CGH ","articletitle":"An integrated genomic analysis of human glioblastoma multiforme.","tags":["cancer","neural"],"anatomical_origin":["Brain"],"name":"parsons2008cgh_public/parsons2008cgh_genomicMatrix","dataproducer":"Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW.","wrangling_procedure":"Twenty-four normalized probe-value flatfiles were sent via Yousendit by the authors, then reconstructed into a single flatfile at UCSC. Probe coordinate mappings were obtained from the UCSC table browser for illumina 1M platform. These were converted to bed15 format using flatfileToBed15 C code.","sample_type":["tumor"],"type":"genomicMatrix","wrangler":"Chris Szeto","version":"2011-11-01","primary_disease":"brain cancer"}

{"assembly":"hg18","author":"Chris Szeto","name":"probeMap/probesAffy100K","type":"probeMap","version":"2012-06-14","label":"Affy Human 100K CGH array (hg18) e.g. SNP_A-1744186"}

{"longTitle":"Glioma CGH (Kotliarov et al. 2006)","cohort":"Glioma (Kotliarov 2006)","url":"http://www.ncbi.nlm.nih.gov/pubmed/17018597","probeMap":"probeMap/probesAffy100K","dataSubType":"copy number","citation":"Cancer Res. 2006 Oct 1;66(19):9428-36.","label":"Kotliarov Glioma CGH","articletitle":"High-resolution global genomic survey of 178 gliomas reveals novel regions of copy number alteration and allelic imbalances.","tags":["cancer","neural"],"anatomical_origin":["Brain"],"name":"kotliarov2006_public/kotliarov2006_genomicMatrix","dataproducer":"Kotliarov Y, Steed ME, Christopher N, Walling J, Su Q, Center A, Heiss J, Rosenblum M, Mikkelsen T, Zenklusen JC, Fine HA.","wrangling_procedure":"Wrangled from separate 50K_Hind and 50K_Xba CEL files obtained from carray (<A HREF=\"https://caarraydb.nci.nih.gov/caarray/publicExperimentDetailAction.do?expId=1015897590932002\">carray entry</A>) using the R aroma.affymetrix package. Quantile normalization was performed, then copy number analyzed using RMA. Chip and fragment length effects were normalized out. A GLAD model was then fitted to make gain and loss calls. Finally, raw copy numbers were extracted for each probeset. The results from each platform were then combined into a 100K file.","sample_type":["tumor"],"type":"genomicMatrix","wrangler":"Chris Szeto","version":"2011-11-01","primary_disease":"brain cancer"}