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Sample GSM985377 Query DataSets for GSM985377
Status Public on Jun 28, 2013
Title x140
Sample type RNA
 
Channel 1
Source name Breast tumor tissue
Organism Homo sapiens
Characteristics group: BRCA1
pam50agilent: Basal
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 A051
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 -0.110524890852788
CGEN_HUMAN_LIB2_6010323346_0 0.424748788925796
CGEN_HUMAN_LIB2_6010325025_0 -1.00092359402478
CGEN_HUMAN_LIB2_6010327581_0 -0.115589654083959
CGEN_HUMAN_LIB2_6010310491_0 -2.54809327511426
CGEN_HUMAN_LIB2_6010320493_0 -0.266414376756457
CGEN_HUMAN_LIB2_6010304084_0 -0.103969161050274
CGEN_HUMAN_LIB2_6010304258_0 0.395696019150676
CGEN_HUMAN_LIB2_6010307791_0 0.11117511553345
CGEN_HUMAN_LIB2_6010325378_0 2.94791937783359
CGEN_HUMAN_LIB2_6010316817_0 -1.40346199155048
CGEN_HUMAN_LIB2_6010304368_0 0.562718091255225
CGEN_HUMAN_LIB2_6010304482_0 -0.447259595720048
CGEN_HUMAN_LIB2_6010311248_0 -0.720114998941856
CGEN_HUMAN_LIB2_6010304197_0 -0.400946318106936
CGEN_HUMAN_LIB2_6010304370_0 0.646685235076261
CGEN_HUMAN_LIB2_6010304087_0 0.625107778686236
CGEN_HUMAN_LIB2_6010304113_0 -0.891154762174201
CGEN_HUMAN_LIB2_6010304519_0 0.550200039983698
CGEN_HUMAN_LIB2_6010304409_0 -0.607515356485783

Total number of rows: 19191

Table truncated, full table size 888 Kbytes.




Supplementary file Size Download File type/resource
GSM985377_x140.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table
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