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Sample GSM985362 Query DataSets for GSM985362
Status Public on Jun 28, 2013
Title x062
Sample type RNA
 
Channel 1
Source name Breast tumor tissue
Organism Homo sapiens
Characteristics group: Sporadic
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 K154
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) martin.larsen@rsyd.dk
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 1.1225170899513
CGEN_HUMAN_LIB2_6010323346_0 0.114205691570503
CGEN_HUMAN_LIB2_6010325025_0 -1.38716266696994
CGEN_HUMAN_LIB2_6010327581_0 1.00236021526224
CGEN_HUMAN_LIB2_6010310491_0 -1.95680079665923
CGEN_HUMAN_LIB2_6010320493_0 -0.755319388494412
CGEN_HUMAN_LIB2_6010304084_0 -0.983626842117421
CGEN_HUMAN_LIB2_6010304258_0 0.368110924102327
CGEN_HUMAN_LIB2_6010307791_0 0.578381648388122
CGEN_HUMAN_LIB2_6010325378_0 0.698249469387507
CGEN_HUMAN_LIB2_6010316817_0 0.177057106590051
CGEN_HUMAN_LIB2_6010304368_0 -0.869548949884707
CGEN_HUMAN_LIB2_6010304482_0 -0.154212429684338
CGEN_HUMAN_LIB2_6010311248_0 -0.302563474984827
CGEN_HUMAN_LIB2_6010304197_0 1.46833774054157
CGEN_HUMAN_LIB2_6010304370_0 0.0174738358106392
CGEN_HUMAN_LIB2_6010304087_0 0.384806402262109
CGEN_HUMAN_LIB2_6010304113_0 1.06370859211397
CGEN_HUMAN_LIB2_6010304519_0 -0.970973187053343
CGEN_HUMAN_LIB2_6010304409_0 -0.167081594503983

Total number of rows: 19191

Table truncated, full table size 885 Kbytes.




Supplementary file Size Download File type/resource
GSM985362_x062.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table
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