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Sample GSM1311575 Query DataSets for GSM1311575
Status Public on Jun 01, 2015
Title x223
Sample type RNA
 
Channel 1
Source name Breast tumor tissue
Organism Homo sapiens
Characteristics group: Sporadic
pam50agilent: Her2
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 K014
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 0.88729488829242
CGEN_HUMAN_LIB2_6010305554_0 -0.59534206452702
CGEN_HUMAN_LIB2_6010316348_0 0.180896653933699
CGEN_HUMAN_LIB2_6010318548_0 0.0929400132560435
CGEN_HUMAN_LIB2_6010322653_0 0.777807541496249
CGEN_HUMAN_LIB2_6010306515_0 0.096650764880528
CGEN_HUMAN_LIB2_6010327270_0 -0.922511667134154
CGEN_HUMAN_LIB2_6010305889_0 -0.186050756380483
CGEN_HUMAN_LIB2_6010322217_0 0.0122487911576955
CGEN_HUMAN_LIB2_6010300416_0 -1.49951789400786
CGEN_HUMAN_LIB2_6010328195_0 2.97833646647371
CGEN_HUMAN_LIB2_6010311510_0 0.148212592598767
CGEN_HUMAN_LIB2_6010306064_0 -0.309727073290235
CGEN_HUMAN_LIB2_6010325142_0 0.222942013437969
CGEN_HUMAN_LIB2_6010326970_0 2.80375948860522
CGEN_HUMAN_LIB2_6010302501_0 0.83725212136263
CGEN_HUMAN_LIB2_6010308530_0 -1.34446349162589
CGEN_HUMAN_LIB2_6010328062_0 -0.272649133814376
CGEN_HUMAN_LIB2_6010328856_0 -0.720403737837117
CGEN_HUMAN_LIB2_6010313980_0 2.39318625777174

Total number of rows: 28919

Table truncated, full table size 1335 Kbytes.




Supplementary file Size Download File type/resource
GSM1311575_x223.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table
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