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Sample GSM40980 Query DataSets for GSM40980
Status Public on May 13, 2005
Title atrial myocardium, atrial fibrillation 1
Sample type RNA
Source name myocardium, right atrial appendage
Organism Homo sapiens
Extracted molecule total RNA
Description Right atrial appendages were obtained from 30 patients undergoing open heart surgery for valve repair or coronary artery bypass grafting. Of these, ten patients had pmAF defined as duration of AF longer than three months as documented by ECG, and 20 patients had no history of AF and were in SR when open heart surgery was performed. Transmural LV tissue was obtained from five non-failing donor hearts which were not transplanted due to palpable coronary calcifications. After excision, all tissue specimens were immediately frozen in liquid nitrogen and stored at -80°C. Total RNA was purified from homogenized deep-frozen tissue samples following the TRIZOL standard protocol as described by the manufacturer (GibcoBRL, Eggenstein, Germany) and quantified by photometry. 150ng total RNA was used for quality control using the RNA 6000 Nano LabChip kit and Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Synthesis of double-stranded cDNA and of biotinylated cRNA probes as well as subsequent steps of hybridization, washing, and staining followed instructions provided by Affymetrix (Affymetrix, Santa Clara, CA, USA). One set of U133A+B chips (together representing 44.928 probe sets) was used for each human heart sample. All U133 GeneChips passed quality control to eliminate scans with abnormal characteristics, i.e. abnormal low or high dynamic range, high perfect match saturation, high pixel noise, grid misalignment problems, and low mean signal to noise ratio. Low level and statistical analysis was done using R 1.8.1. Microarray data of all atrial and ventricular samples was normalized simultaneously using robust multi-array average (RMA) implemented in Bioconductor's "affy"-package.
Keywords = Homo sapiens, myocardial tissue, comparison of right atrial tissue of patients of patients with atrial fibrillation and sinus rhythm with left ventricular gene expression
Submission date Feb 03, 2005
Last update date Oct 28, 2005
Contact name Andreas S. Barth
Phone 0049-(0)89-7095-0
Organization name University of Munich (LMU), Grosshadern
Department Department of Cardiology
Street address Marchioninistr. 15
City Munich
ZIP/Postal code 81377
Country Germany
Platform ID GPL96
Series (1)
GSE2240 Comparison of atrial tissue of patients with atrial fibrillation and sinus rhythm with ventricular gene expression

Data table header descriptions
ID_REF Affymetrix probe set ID
VALUE 'signal' a measure of the abundance of a transcript (after normalization with robust-multiarray average (RMA) implemented in Bioconductor's affy-package)
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M).
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call, as calculated by the Bioconductor's affy-package.

Data table
1007_s_at 9.952724878 P 0.00222774
1053_at 6.326668081 P 0.039365362
117_at 7.65391674 P 0.014936519
121_at 9.803071447 P 0.021866375
1255_g_at 5.371315529 A 0.150527117
1294_at 8.259985552 P 0.014936519
1316_at 6.902687862 P 0.009985415
1320_at 7.553970984 M 0.043967773
1405_i_at 6.701270765 A 0.128890796
1431_at 5.356873646 A 0.081336714
1438_at 7.877952969 A 0.621815485
1487_at 9.32377624 P 0.014936519
1494_f_at 8.098739085 M 0.054470435
1598_g_at 11.56971109 P 0.000467603
160020_at 8.630286582 P 0.019303461
1729_at 8.662218974 A 0.189687302
177_at 6.667039824 P 0.00868917
1773_at 7.585806671 P 0.004180367
179_at 10.64538809 P 0.039365362
1861_at 7.07745708 P 0.014936519

Total number of rows: 22283

Table truncated, full table size 797 Kbytes.

Supplementary file Size Download File type/resource
GSM40980.CEL.gz 3.6 Mb (ftp)(http) CEL

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