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Sample GSM1311488

Query DataSets for GSM1311488

Status

Public on Jun 01, 2015

Title

x314

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

Characteristics

group: BRCA2
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

A011

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	0.868132702146942
CGEN_HUMAN_LIB2_6010305554_0	-0.719013456643517
CGEN_HUMAN_LIB2_6010316348_0	0.134211672469651
CGEN_HUMAN_LIB2_6010318548_0	0.32211576248879
CGEN_HUMAN_LIB2_6010322653_0	0.350021039940131
CGEN_HUMAN_LIB2_6010306515_0	0.40641262020101
CGEN_HUMAN_LIB2_6010327270_0	-0.715563718229832
CGEN_HUMAN_LIB2_6010305889_0	-0.220372504464205
CGEN_HUMAN_LIB2_6010322217_0	-0.205642326568251
CGEN_HUMAN_LIB2_6010300416_0	-0.960344109746529
CGEN_HUMAN_LIB2_6010328195_0	4.59964432116994
CGEN_HUMAN_LIB2_6010311510_0	-0.165345922960308
CGEN_HUMAN_LIB2_6010306064_0	-0.526558931350973
CGEN_HUMAN_LIB2_6010325142_0	-0.201675306804724
CGEN_HUMAN_LIB2_6010326970_0	0.903550991693443
CGEN_HUMAN_LIB2_6010302501_0	-0.569784103959889
CGEN_HUMAN_LIB2_6010308530_0	-1.32243667093275
CGEN_HUMAN_LIB2_6010328062_0	0.0409767017414491
CGEN_HUMAN_LIB2_6010328856_0	-0.675884676123301
CGEN_HUMAN_LIB2_6010313980_0	0.0456677254205197

Total number of rows: 28919

Table truncated, full table size 1335 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1311488_x314.gpr.gz	2.8 Mb	(ftp)(http)	GPR
Processed data included within Sample table

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