Comment[ArrayExpressAccession] E-GEOD-51697 MAGE-TAB Version 1.1 Public Release Date 2013-11-20 Investigation Title The effect of imatinib therapy on tumor associated macrophages (TAMs) in human gastrointestinal stromal tumor (GIST) Comment[Submitted Name] The effect of imatinib therapy on tumor associated macrophages (TAMs) in human gastrointestinal stromal tumor (GIST) Experiment Description The gene expression profile of TAMs microbead isolated from freshly obtained human GISTs were compared in tumors that were untreated, responding to imatinib (sensitive), or resistant to imatinib (resistant) The Affymetrix Human Genome U133A 2.0 platform was used TAMs were microbead isolated from 12 untreated, 5 sensitive, and 4 resistant tumors. Tumors were obtained freshly from the operating room from consenting patients using an IRB approved protocol. Tumors were digested using collagenase and TAMs isolated using microbead negative selection for KIT, CD3, and CD56 followed by positive selection for CD14. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Zhao Cavnar Zeng Kim Sorenson Ocuin Balachandran Seifert Greer Popow Crawley Cohen Green Rossi Besmer Antonescu DeMatteo Person First Name Jeffrey Michael Shan Teresa Eric Lee Vinod Adrian Jonathan Rachel Megan Noah Benjamin Ferdinand Peter Cristina Ronald Person Mid Initials J S C M P M B H A L R P Person Email zhaoy@mskcc.org Person Affiliation Memorial Sloan Kettering Cancer Center Person Address Genomics Core, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA Person Roles submitter Protocol Name P-GSE51697-1 P-GSE51697-5 P-GSE51697-6 P-GSE51697-2 P-GSE51697-3 P-GSE51697-4 P-GSE51697-7 Protocol Description Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. The data were analyzed with MAS 5.0 algorithm using Affymetrix Gene Expression Console. ID_REF = VALUE = MAS 5.0 ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described). 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450. Tumors were obtained from humans diagnosed with GIST that were untreated, or sensitive to imatinib, or resistant to imatinib based on RECIST criteria. Tumors were obtained freshly from the operating room from consenting patients using an IRB approved protocol. RNeasy Plus Mini Kit (Qiagen) was used to isolate RNA. Affymetrix GeneArray scanner 7G Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol growth protocol nucleic acid extraction protocol array scanning protocol Comment[SecondaryAccession] GSE51697 Comment[GEOReleaseDate] 2013-11-20 Comment[ArrayExpressSubmissionDate] 2013-10-25 Comment[GEOLastUpdateDate] 2013-11-22 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-51697.sdrf.txt