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E-GEOD-59772.idf.txt
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25 lines (25 loc) · 2.37 KB
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Comment[ArrayExpressAccession] E-GEOD-59772
MAGE-TAB Version 1.1
Public Release Date 2015-05-01
Investigation Title Analysis of compartment-specific gene expression in breast cancer tumors
Comment[Submitted Name] Analysis of compartment-specific gene expression in breast cancer tumors
Experiment Description Triple-negative primary breast cancer tumors, rich in inflammatory stroma, were laser microdissected and global mRNA expression was analyzed in stroma compartment, cancer cell compartment, and in total tumor tissue. Three FFPE breast cancer tumors wer laser microdissected and the cancer cell and stroma compartments were collected. A piece of t
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 Larsson Winslow Leandersson Edsjö Larsson
Person First Name Christer Sofia Karin Anders Christer
Person Email christer.larsson@med.lu.se
Person Affiliation Lund university
Person Address Laboratory Medicine, Lund university, Medicon Village, Bldg 404:C3, Lund, Sweden
Person Roles submitter
Protocol Name P-GSE59772-1 P-GSE59772-3 P-GSE59772-4 P-GSE59772-2 P-GSE59772-5
Protocol Description The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method. ID_REF = VALUE = log2 GC-RMA signal Biotinylated cDNA were prepared according to the SensationPlus FFPE Affymetrix protocol from approximately 100 ng total RNA (SensationPlus FFPE Amplification and WT labeling kit User guide, 2012, Affymetrix). Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 47C on GeneChip Human Gene 1.0 ST array in GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Qiagen AllPrep DNA/RNA FFPE kit GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
Protocol Type normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol
Experimental Factor Name organism part
Experimental Factor Type organism part
Comment[SecondaryAccession] GSE59772
Comment[GEOReleaseDate] 2015-05-01
Comment[ArrayExpressSubmissionDate] 2014-07-25
Comment[GEOLastUpdateDate] 2015-05-08
Comment[AEExperimentType] transcription profiling by array
SDRF File E-GEOD-59772.sdrf.txt