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Sample GSM1311499

Query DataSets for GSM1311499

Status

Public on Jun 01, 2015

Title

x079R

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

Characteristics

group: BRCAx
pam50agilent: Basal

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

A037

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	0.072095738525308
CGEN_HUMAN_LIB2_6010305554_0	-0.817242812261641
CGEN_HUMAN_LIB2_6010316348_0	-0.0764921021650456
CGEN_HUMAN_LIB2_6010318548_0	0.0935870622749865
CGEN_HUMAN_LIB2_6010322653_0	0.345598021417144
CGEN_HUMAN_LIB2_6010306515_0	0.26025136128777
CGEN_HUMAN_LIB2_6010327270_0	-0.519000413023596
CGEN_HUMAN_LIB2_6010305889_0	-0.139083127022941
CGEN_HUMAN_LIB2_6010322217_0	-0.147274303038314
CGEN_HUMAN_LIB2_6010300416_0	-0.691558972850982
CGEN_HUMAN_LIB2_6010328195_0	3.98486831480581
CGEN_HUMAN_LIB2_6010311510_0	-0.168448851153637
CGEN_HUMAN_LIB2_6010306064_0	-0.282476459043414
CGEN_HUMAN_LIB2_6010325142_0	-0.130184539584956
CGEN_HUMAN_LIB2_6010326970_0	1.61220456983897
CGEN_HUMAN_LIB2_6010302501_0	1.8948614408458
CGEN_HUMAN_LIB2_6010308530_0	-1.40280906341729
CGEN_HUMAN_LIB2_6010328062_0	-0.0684541552450231
CGEN_HUMAN_LIB2_6010328856_0	-0.35457929806554
CGEN_HUMAN_LIB2_6010313980_0	0.438799574597001

Total number of rows: 28919

Table truncated, full table size 1338 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1311499_x079R.gpr.gz	2.8 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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