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Sample GSM1311573 Query DataSets for GSM1311573
Status Public on Jun 01, 2015
Title x177
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 K007
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 1.1435336124586
CGEN_HUMAN_LIB2_6010305554_0 0.0992769524697547
CGEN_HUMAN_LIB2_6010316348_0 0.163013399685331
CGEN_HUMAN_LIB2_6010318548_0 0.20615423003455
CGEN_HUMAN_LIB2_6010322653_0 0.675260135002795
CGEN_HUMAN_LIB2_6010306515_0 0.614773774509337
CGEN_HUMAN_LIB2_6010327270_0 -1.05468505399705
CGEN_HUMAN_LIB2_6010305889_0 0.357286321374833
CGEN_HUMAN_LIB2_6010322217_0 0.157867691977509
CGEN_HUMAN_LIB2_6010300416_0 -0.785614577919753
CGEN_HUMAN_LIB2_6010328195_0 3.87830664095357
CGEN_HUMAN_LIB2_6010311510_0 0.0369707093003449
CGEN_HUMAN_LIB2_6010306064_0 0.527244824087055
CGEN_HUMAN_LIB2_6010325142_0 -0.212817494651645
CGEN_HUMAN_LIB2_6010326970_0 4.50108487654651
CGEN_HUMAN_LIB2_6010302501_0 1.50369532605717
CGEN_HUMAN_LIB2_6010308530_0 -0.829529629285305
CGEN_HUMAN_LIB2_6010328062_0 0.665640535864528
CGEN_HUMAN_LIB2_6010328856_0 -0.0623953321173518
CGEN_HUMAN_LIB2_6010313980_0 0.852559321221215

Total number of rows: 28919

Table truncated, full table size 1335 Kbytes.




Supplementary file Size Download File type/resource
GSM1311573_x177.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table
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