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Sample GSM1311535

Query DataSets for GSM1311535

Status

Public on Jun 01, 2015

Title

x111R

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

Characteristics

group: BRCAx
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

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

A097

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

Series (1)

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	0.640369103833773
CGEN_HUMAN_LIB2_6010305554_0	0.558250000216057
CGEN_HUMAN_LIB2_6010316348_0	-0.112173242129436
CGEN_HUMAN_LIB2_6010318548_0	0.0701342538693084
CGEN_HUMAN_LIB2_6010322653_0	0.651473366656167
CGEN_HUMAN_LIB2_6010306515_0	0.131908235617159
CGEN_HUMAN_LIB2_6010327270_0	-0.229490775466634
CGEN_HUMAN_LIB2_6010305889_0	-0.169788818166502
CGEN_HUMAN_LIB2_6010322217_0	0.241284326932126
CGEN_HUMAN_LIB2_6010300416_0	-0.8096952780538
CGEN_HUMAN_LIB2_6010328195_0	3.73884764965758
CGEN_HUMAN_LIB2_6010311510_0	-0.164006396109198
CGEN_HUMAN_LIB2_6010306064_0	0.221656985693745
CGEN_HUMAN_LIB2_6010325142_0	0.450467336302187
CGEN_HUMAN_LIB2_6010326970_0	1.88810263630828
CGEN_HUMAN_LIB2_6010302501_0	0.179349546665351
CGEN_HUMAN_LIB2_6010308530_0	-0.401330720797892
CGEN_HUMAN_LIB2_6010328062_0	-0.0808697623610903
CGEN_HUMAN_LIB2_6010328856_0	-0.0908827243826253
CGEN_HUMAN_LIB2_6010313980_0	0.180589471779526

Total number of rows: 28919

Table truncated, full table size 1338 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1311535_x111R.gpr.gz	2.7 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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