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Sample GSM985391

Query DataSets for GSM985391

Status

Public on Jun 28, 2013

Title

x190

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

Characteristics

group: Sporadic
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

K080

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

Aug 14, 2012

Last update date

Jun 28, 2013

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 (2)

GSE40115	Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling
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_6010315280_0	0.284925747272235
CGEN_HUMAN_LIB2_6010323346_0	0.204969886710751
CGEN_HUMAN_LIB2_6010325025_0	-1.45462722489101
CGEN_HUMAN_LIB2_6010327581_0	-0.469657812725484
CGEN_HUMAN_LIB2_6010310491_0	-2.409083381822
CGEN_HUMAN_LIB2_6010320493_0	-0.148063547842766
CGEN_HUMAN_LIB2_6010304084_0	-0.229055646179733
CGEN_HUMAN_LIB2_6010304258_0	-0.517756569429226
CGEN_HUMAN_LIB2_6010307791_0	-0.424129286697686
CGEN_HUMAN_LIB2_6010325378_0	-0.00331535182203258
CGEN_HUMAN_LIB2_6010316817_0	0.640862470986589
CGEN_HUMAN_LIB2_6010304368_0	-0.747325457890833
CGEN_HUMAN_LIB2_6010304482_0	-0.0722656910955754
CGEN_HUMAN_LIB2_6010311248_0	-0.438888219820087
CGEN_HUMAN_LIB2_6010304197_0	0.520955974924634
CGEN_HUMAN_LIB2_6010304370_0	-0.757521489418584
CGEN_HUMAN_LIB2_6010304087_0	0.117461113801644
CGEN_HUMAN_LIB2_6010304113_0	1.03021364947452
CGEN_HUMAN_LIB2_6010304519_0	-1.06440421061157
CGEN_HUMAN_LIB2_6010304409_0	0.594897493719551

Total number of rows: 19191

Table truncated, full table size 888 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM985391_x190.gpr.gz	2.7 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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