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Sample GSM1311616

Query DataSets for GSM1311616

Status

Public on Jun 01, 2015

Title

x181

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

Characteristics

group: Sporadic
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

K156

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	0.692102055852096
CGEN_HUMAN_LIB2_6010305554_0	-0.0726982463871593
CGEN_HUMAN_LIB2_6010316348_0	0.0279140581785953
CGEN_HUMAN_LIB2_6010318548_0	0.109513736636442
CGEN_HUMAN_LIB2_6010322653_0	0.435556287431751
CGEN_HUMAN_LIB2_6010306515_0	0.705387001919778
CGEN_HUMAN_LIB2_6010327270_0	-0.526500288609446
CGEN_HUMAN_LIB2_6010305889_0	-0.00352002111241592
CGEN_HUMAN_LIB2_6010322217_0	0.229932407537081
CGEN_HUMAN_LIB2_6010300416_0	-0.351839954189597
CGEN_HUMAN_LIB2_6010328195_0	4.71471995745493
CGEN_HUMAN_LIB2_6010311510_0	0.411141134861388
CGEN_HUMAN_LIB2_6010306064_0	-0.0411924013066481
CGEN_HUMAN_LIB2_6010325142_0	0.203390058471094
CGEN_HUMAN_LIB2_6010326970_0	1.67729463778564
CGEN_HUMAN_LIB2_6010302501_0	-0.16470195653755
CGEN_HUMAN_LIB2_6010308530_0	-1.04553626709279
CGEN_HUMAN_LIB2_6010328062_0	0.0103527254995544
CGEN_HUMAN_LIB2_6010328856_0	-0.644532428837809
CGEN_HUMAN_LIB2_6010313980_0	0.0783110019305318

Total number of rows: 28919

Table truncated, full table size 1336 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1311616_x181.gpr.gz	2.7 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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