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Sample GSM1311502

Query DataSets for GSM1311502

Status

Public on Jun 01, 2015

Title

x116R

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

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

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

A043

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	1.62885421564856
CGEN_HUMAN_LIB2_6010305554_0	-0.784265293204938
CGEN_HUMAN_LIB2_6010316348_0	-0.441226754200224
CGEN_HUMAN_LIB2_6010318548_0	0.0489131381820933
CGEN_HUMAN_LIB2_6010322653_0	0.461523314315453
CGEN_HUMAN_LIB2_6010306515_0	0.326050473309211
CGEN_HUMAN_LIB2_6010327270_0	-1.61070693201601
CGEN_HUMAN_LIB2_6010305889_0	0.695396359757778
CGEN_HUMAN_LIB2_6010322217_0	0.491193997072974
CGEN_HUMAN_LIB2_6010300416_0	-0.763912303463476
CGEN_HUMAN_LIB2_6010328195_0	2.9766053585607
CGEN_HUMAN_LIB2_6010311510_0	0.0795783556884883
CGEN_HUMAN_LIB2_6010306064_0	-0.0355659021145207
CGEN_HUMAN_LIB2_6010325142_0	-0.132176464568778
CGEN_HUMAN_LIB2_6010326970_0	1.64847525017705
CGEN_HUMAN_LIB2_6010302501_0	0.39298709796365
CGEN_HUMAN_LIB2_6010308530_0	-0.987129056584102
CGEN_HUMAN_LIB2_6010328062_0	-0.164696871094364
CGEN_HUMAN_LIB2_6010328856_0	-0.592338669624753
CGEN_HUMAN_LIB2_6010313980_0	0.252368960898494

Total number of rows: 28919

Table truncated, full table size 1334 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1311502_x116R.gpr.gz	2.7 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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