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Sample GSM985408 Query DataSets for GSM985408
Status Public on Jun 28, 2013
Title x259
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 K083
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 -0.00667541056287979
CGEN_HUMAN_LIB2_6010323346_0 0.0315299642864849
CGEN_HUMAN_LIB2_6010325025_0 -1.48024135839771
CGEN_HUMAN_LIB2_6010327581_0 -0.126275542839749
CGEN_HUMAN_LIB2_6010310491_0 -2.10593892403203
CGEN_HUMAN_LIB2_6010320493_0 -0.347313919658839
CGEN_HUMAN_LIB2_6010304084_0 -0.304521982765471
CGEN_HUMAN_LIB2_6010304258_0 0.148463785852374
CGEN_HUMAN_LIB2_6010307791_0 0.455803903868284
CGEN_HUMAN_LIB2_6010325378_0 1.38277309527689
CGEN_HUMAN_LIB2_6010316817_0 1.60512983764686
CGEN_HUMAN_LIB2_6010304368_0 0.161552528391893
CGEN_HUMAN_LIB2_6010304482_0 0.116959611181331
CGEN_HUMAN_LIB2_6010311248_0 -0.900740580718365
CGEN_HUMAN_LIB2_6010304197_0 0.359133709519959
CGEN_HUMAN_LIB2_6010304370_0 -0.0246378257560048
CGEN_HUMAN_LIB2_6010304087_0 0.148340796213574
CGEN_HUMAN_LIB2_6010304113_0 1.99543409182596
CGEN_HUMAN_LIB2_6010304519_0 -0.397465771279592
CGEN_HUMAN_LIB2_6010304409_0 0.0402258539496736

Total number of rows: 19191

Table truncated, full table size 888 Kbytes.




Supplementary file Size Download File type/resource
GSM985408_x259.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table
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