Tier1 mutations in the PCGP project public data

{"cgdataversion":1,"longTitle":"TARGET acute lymphoblastic leukemia copy number variation","cohort":"TARGET Acute Lymphoblastic Leukemia","url":"ftp://caftpd.nci.nih.gov/pub/dcc_target/ALL/copy_number_array/","probeMap":"TARGET_ALL/probesTARGETcnv","dataSubType":"copy number","citation":"Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9414-8. Epub 2009 May 22.","label":"TARGET acute lymphoblastic leukemia copy number","articletitle":"JAK mutations in high-risk childhood acute lymphoblastic leukemia.","tags":["white blood cell","pediatrics","cancer"],"anatomical_origin":["Blood"],"name":"TARGET_ALL/TARGETcnv_genomicMatrix","dataproducer":"Mullighan CG, Zhang J, Harvey RC, Collins-Underwood JR, Schulman BA, Phillips LA, Tasian SK, Loh ML, Su X, Liu W, Devidas M, Atlas SR, Chen IM, Clifford RJ, Gerhard DS, Carroll WL, Reaman GH, Smith M, Downing JR, Hunger SP, Willman CL.","wrangling_procedure":"Segmented data obtained from caGrid (<A HREF=\"https://ocg.cancer.gov/programs/target/data-matrix\">Link to data portal</A>). Data was converted to a zero-centered log-scale, then converted to bed15 format for uploading using segToBed.py script developed by J. Zack Sanborn.","sample_type":["tumor"],"groupTitle":" Treehouse Childhood Cancer","type":"genomicMatrix","wrangler":"Chris Szeto","version":"2011-11-01","shortTitle":"Treehouse - TARGET acute lymphoblastic leukemia copy number","primary_disease":"childhood acute lymphoblastic leukemia"}

TARGET acute lymphoblastic leukemia copy number variation

{"cgdataversion":1,"longTitle":"TARGET Acute Lymphoblastic Leukemia gene expression","cohort":"TARGET Acute Lymphoblastic Leukemia","url":"ftp://caftpd.nci.nih.gov/pub/dcc_target/ALL/gene_expression_array/","probeMap":"probeMap/affyU133_ucscGenomeBrowser_hg18.probeMap","dataSubType":"gene expression","citation":"Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9414-8. Epub 2009 May 22.","label":"TARGET acute lymphoblastic leukemia expression","articletitle":"JAK mutations in high-risk childhood acute lymphoblastic leukemia.","tags":["cancer"],"anatomical_origin":["Blood"],"name":"TARGET_ALL/TARGETexp_genomicMatrix","dataproducer":"Mullighan CG, Zhang J, Harvey RC, Collins-Underwood JR, Schulman BA, Phillips LA, Tasian SK, Loh ML, Su X, Liu W, Devidas M, Atlas SR, Chen IM, Clifford RJ, Gerhard DS, Carroll WL, Reaman GH, Smith M, Downing JR, Hunger SP, Willman CL.","wrangling_procedure":"Obtained HG-U133 plus 2.0 .CEL files from caGrid (<A HREF=\"https://ocg.cancer.gov/programs/target/data-matrix\">Link to data portal</A>). These were processed into log2 ratios using the R package \"affy\" using RMA normalization and probe-level mean-centering. The resulting matrix file was mapped to genome coordinates (i.e. bed15 format) using the positions given by affymetrix (<A HREF=\"http://www.affymetrix.com/products_services/arrays/specific/hgu133plus.affx#1_4\">link to affymetrix data page</A>) and the program flatfileToBed15 developed by Chris Szeto.","sample_type":["tumor"],"type":"genomicMatrix","wrangler":"Chris Szeto","version":"2011-11-01","gdata_tags":["transcription","mRNA"],"shortTitle":"Treehouse - TARGET acute lymphoblastic leukemia expression","primary_disease":"childhood acute lymphoblastic leukemia"}