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Sample GSM41106 Query DataSets for GSM41106
Status Public on May 13, 2005
Title atrial myocardium, sinus rhythm 12B
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 permanent AF defined as duration of AF longer than three months as documented by ECG, and 20 patients had no history of AF and were in sinus rhythm 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 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
E-mail(s) andreas.barth@med.uni-muenchen.de
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 GPL97
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
200000_s_at 10.26224561 P 0.001641799
200001_at 12.12283046 P 0.002180626
200002_at 11.61486442 P 0.001641799
200003_s_at 11.39555051 P 0.001641799
200004_at 11.85373335 P 0.001641799
200005_at 10.37688541 P 0.002180626
200006_at 11.7636606 P 0.002180626
200007_at 11.52197859 P 0.001641799
200008_s_at 10.70907877 P 0.001641799
200009_at 11.19114948 P 0.001641799
200010_at 12.20580004 P 0.001641799
200011_s_at 10.21011291 P 0.003763203
200012_x_at 12.94106887 P 0.001641799
200013_at 12.31909473 P 0.001641799
200014_s_at 10.01474191 P 0.001641799
200015_s_at 9.779757247 P 0.002875125
200016_x_at 12.38438754 P 0.001641799
200017_at 12.2393967 P 0.002180626
200018_at 12.99975448 P 0.001641799
200019_s_at 11.80154146 P 0.001641799

Total number of rows: 22645

Table truncated, full table size 797 Kbytes.




Supplementary file Size Download File type/resource
GSM41106.CEL.gz 3.6 Mb (ftp)(http) CEL

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