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Sample GSM985360

Query DataSets for GSM985360

Status

Public on Jun 28, 2013

Title

x056

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

Characteristics

group: BRCA2
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

A003

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	0.42252983959236
CGEN_HUMAN_LIB2_6010323346_0	0.291106119538884
CGEN_HUMAN_LIB2_6010325025_0	-0.917445252386821
CGEN_HUMAN_LIB2_6010327581_0	0.610271267731228
CGEN_HUMAN_LIB2_6010310491_0	-2.09661860655531
CGEN_HUMAN_LIB2_6010320493_0	0.113727776229373
CGEN_HUMAN_LIB2_6010304084_0	-0.663265824130932
CGEN_HUMAN_LIB2_6010304258_0	-0.249814834602946
CGEN_HUMAN_LIB2_6010307791_0	0.646730475738492
CGEN_HUMAN_LIB2_6010325378_0	0.159675026063849
CGEN_HUMAN_LIB2_6010316817_0	0.745664190310088
CGEN_HUMAN_LIB2_6010304368_0	-0.564395090825087
CGEN_HUMAN_LIB2_6010304482_0	0.414760241511102
CGEN_HUMAN_LIB2_6010311248_0	-0.398585369245911
CGEN_HUMAN_LIB2_6010304197_0	-0.0785502268317744
CGEN_HUMAN_LIB2_6010304370_0	-0.255672657147625
CGEN_HUMAN_LIB2_6010304087_0	-0.10411690263609
CGEN_HUMAN_LIB2_6010304113_0	2.23996817041612
CGEN_HUMAN_LIB2_6010304519_0	-0.703733659239008
CGEN_HUMAN_LIB2_6010304409_0	0.41413671043613

Total number of rows: 19191

Table truncated, full table size 887 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM985360_x056.gpr.gz	2.7 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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