GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1311553

Query DataSets for GSM1311553

Status

Public on Jun 01, 2015

Title

x152

Sample type

RNA

Channel 1

Source name

Breast tumor tissue

Organism

Characteristics

group: BRCAx
pam50agilent: Her2

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

A139

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	0.641678872935788
CGEN_HUMAN_LIB2_6010305554_0	-0.508615598744895
CGEN_HUMAN_LIB2_6010316348_0	0.0964102483645311
CGEN_HUMAN_LIB2_6010318548_0	0.0413964717345264
CGEN_HUMAN_LIB2_6010322653_0	0.356999494825598
CGEN_HUMAN_LIB2_6010306515_0	0.51651616551399
CGEN_HUMAN_LIB2_6010327270_0	-1.26038356507036
CGEN_HUMAN_LIB2_6010305889_0	0.187980047349328
CGEN_HUMAN_LIB2_6010322217_0	0.0501357204210315
CGEN_HUMAN_LIB2_6010300416_0	-1.3294208089165
CGEN_HUMAN_LIB2_6010328195_0	5.22525515873731
CGEN_HUMAN_LIB2_6010311510_0	0.156916898158174
CGEN_HUMAN_LIB2_6010306064_0	0.889635070227092
CGEN_HUMAN_LIB2_6010325142_0	0.0663488693684848
CGEN_HUMAN_LIB2_6010326970_0	3.20543150689771
CGEN_HUMAN_LIB2_6010302501_0	-0.456131370342579
CGEN_HUMAN_LIB2_6010308530_0	-1.02005233567155
CGEN_HUMAN_LIB2_6010328062_0	-0.227289318998528
CGEN_HUMAN_LIB2_6010328856_0	-0.394076607534449
CGEN_HUMAN_LIB2_6010313980_0	0.466857034886679

Total number of rows: 28919

Table truncated, full table size 1336 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1311553_x152.gpr.gz	2.7 Mb	(ftp)(http)	GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |