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Sample GSM1311562 Query DataSets for GSM1311562
Status Public on Jun 01, 2015
Title x248
Sample type RNA
 
Channel 1
Source name Breast tumor tissue
Organism Homo sapiens
Characteristics group: BRCAx
pam50agilent: LumA
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 A161
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 Jan 22, 2014
Last update date Jun 01, 2015
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 (1)
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_6010321789_0 0.562275041873694
CGEN_HUMAN_LIB2_6010305554_0 0.0547677333059173
CGEN_HUMAN_LIB2_6010316348_0 1.20647029172919
CGEN_HUMAN_LIB2_6010318548_0 0.0592813002761627
CGEN_HUMAN_LIB2_6010322653_0 0.501025868121547
CGEN_HUMAN_LIB2_6010306515_0 0.26717544738307
CGEN_HUMAN_LIB2_6010327270_0 -0.582767334625644
CGEN_HUMAN_LIB2_6010305889_0 -0.231498371994971
CGEN_HUMAN_LIB2_6010322217_0 0.065894031683104
CGEN_HUMAN_LIB2_6010300416_0 -0.588957134566003
CGEN_HUMAN_LIB2_6010328195_0 3.65829377571968
CGEN_HUMAN_LIB2_6010311510_0 0.547901883975397
CGEN_HUMAN_LIB2_6010306064_0 0.414095333071617
CGEN_HUMAN_LIB2_6010325142_0 -0.0606905147373283
CGEN_HUMAN_LIB2_6010326970_0 1.99761350427459
CGEN_HUMAN_LIB2_6010302501_0 0.0749449135214549
CGEN_HUMAN_LIB2_6010308530_0 -1.22235933869183
CGEN_HUMAN_LIB2_6010328062_0 -0.281607985334063
CGEN_HUMAN_LIB2_6010328856_0 -0.222307694892869
CGEN_HUMAN_LIB2_6010313980_0 0.191655925903998

Total number of rows: 28919

Table truncated, full table size 1335 Kbytes.




Supplementary file Size Download File type/resource
GSM1311562_x248.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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