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Sample GSM985357 Query DataSets for GSM985357
Status Public on Jun 28, 2013
Title x051
Sample type RNA
 
Channel 1
Source name Breast tumor tissue
Organism Homo sapiens
Characteristics group: BRCA2
pam50agilent: LumB
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).
Label Cy5
Label protocol RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.
 
Channel 2
Source name Universal Human Reference RNA (Stratagene)
Organism Homo sapiens
Characteristics reference: Universal Human Reference RNA (Stratagene)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).
Label Cy3
Label protocol RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.
 
 
Hybridization protocol Fragmentation, hybridization and washing for the spotted arrays were carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies ) and Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocol in a low ozone environment.
Scan protocol Scanned using a Agilent G2565CA Microarray scanner
Description A102
Data processing Scanned images were quantified by Gene Pix Pro 6.0 (Molecular Devices). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. The 92 samples were processed together with 154 other breast tumor samples. ComBat method was used for adjustment of the batch effects across the different spotting batches [PMID: 16632515]. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).
 
Submission date Aug 14, 2012
Last update date Jun 28, 2013
Contact name Martin Jakob Larsen
E-mail(s) [email protected]
Organization name Odense University Hospital
Department Dept. of Clinical Genetics
Street address Sdr. Boulevard 29
City Odense C
ZIP/Postal code 5000
Country Denmark
 
Platform ID GPL15932
Series (2)
GSE40115 Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling
GSE54275 Microarray gene expression analysis: Batch effect removal improves the cross-platform consistency

Data table header descriptions
ID_REF
VALUE Log2 transformed ratios(Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
CGEN_HUMAN_LIB2_6010315280_0 0.265620893589075
CGEN_HUMAN_LIB2_6010323346_0 0.697425668629265
CGEN_HUMAN_LIB2_6010325025_0 -1.11364055823037
CGEN_HUMAN_LIB2_6010327581_0 0.36876351530346
CGEN_HUMAN_LIB2_6010310491_0 -1.85627393073022
CGEN_HUMAN_LIB2_6010320493_0 0.242967525696969
CGEN_HUMAN_LIB2_6010304084_0 -0.487219460287891
CGEN_HUMAN_LIB2_6010304258_0 -0.193884176484209
CGEN_HUMAN_LIB2_6010307791_0 0.0298440802652754
CGEN_HUMAN_LIB2_6010325378_0 0.603165335820068
CGEN_HUMAN_LIB2_6010316817_0 0.326291697296497
CGEN_HUMAN_LIB2_6010304368_0 -0.387664093250824
CGEN_HUMAN_LIB2_6010304482_0 0.633330835493029
CGEN_HUMAN_LIB2_6010311248_0 0.329740563202408
CGEN_HUMAN_LIB2_6010304197_0 1.68180114608494
CGEN_HUMAN_LIB2_6010304370_0 -0.482152999066172
CGEN_HUMAN_LIB2_6010304087_0 -0.561407825550912
CGEN_HUMAN_LIB2_6010304113_0 1.2662092064072
CGEN_HUMAN_LIB2_6010304519_0 -0.953240413229042
CGEN_HUMAN_LIB2_6010304409_0 0.461165616234542

Total number of rows: 19191

Table truncated, full table size 887 Kbytes.




Supplementary file Size Download File type/resource
GSM985357_x051.gpr.gz 2.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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