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Sample GSM985406

Query DataSets for GSM985406

Status

Public on Jun 28, 2013

Title

x253

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

K120

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	1.57887581525598
CGEN_HUMAN_LIB2_6010323346_0	-0.0435030257284698
CGEN_HUMAN_LIB2_6010325025_0	-1.1069867719443
CGEN_HUMAN_LIB2_6010327581_0	-0.204204600604773
CGEN_HUMAN_LIB2_6010310491_0	-2.46431425062129
CGEN_HUMAN_LIB2_6010320493_0	-0.301607460859613
CGEN_HUMAN_LIB2_6010304084_0	-0.496833250792485
CGEN_HUMAN_LIB2_6010304258_0	-0.178097766444678
CGEN_HUMAN_LIB2_6010307791_0	-0.221081679367837
CGEN_HUMAN_LIB2_6010325378_0	-0.0583867049318507
CGEN_HUMAN_LIB2_6010316817_0	-0.15719857847836
CGEN_HUMAN_LIB2_6010304368_0	-0.328721661052843
CGEN_HUMAN_LIB2_6010304482_0	0.103700892951068
CGEN_HUMAN_LIB2_6010311248_0	-0.397332297238144
CGEN_HUMAN_LIB2_6010304197_0	2.02650651404136
CGEN_HUMAN_LIB2_6010304370_0	-0.38152957351823
CGEN_HUMAN_LIB2_6010304087_0	0.143580163928774
CGEN_HUMAN_LIB2_6010304113_0	1.15265006769783
CGEN_HUMAN_LIB2_6010304519_0	-0.500819683877017
CGEN_HUMAN_LIB2_6010304409_0	0.60321398079763

Total number of rows: 19191

Table truncated, full table size 887 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM985406_x253.gpr.gz	2.8 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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