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Sample GSM539525 Query DataSets for GSM539525
Status Public on May 01, 2010
Title SCO_2
Sample type RNA
 
Source name testicular biopsy
Organism Homo sapiens
Characteristics deletion: control
histology: SCO
Treatment protocol Testicular biopsies were obtained from open surgery and classified based on homogeneous histology with no discrepancy to paralle biopsies and test-TESE.
Extracted molecule total RNA
Extraction protocol Biopsies were homogeneized in RNApure (Peqlab, Germany) with an Ultra-Thurrax and total RNA repurified on RNeasy columns (Qiagen, Germany). Quality control was done with a Bioanalyzer (Agilent, USA).
Label Cy5
Label protocol total RNA was amplified with the MessageAmp III Kit (Ambion, USA) and Biotin-UTP incorporated as a label.
 
Hybridization protocol Hybridization was conducted for 20h at 37°C and arrays washed in 1x TNT (10 min, RT) and 1x TNT (60 min, 46°C). Staining with Cy5-Streptavidin was done for 30 min at RT. Then, arrays were washed 2 times with 1x TNT for 10 min and 0.2x SSPE for 30s. They were spin-dried in a centrifuge at 2000 rpm for 2 min.
Scan protocol Scanning was done on an Affymetrix 428 Scanner (Affymetrix, USA) at PMT 70 settings using the Jaguar 2.0 software for image acquisition.
Description Patient with Sertoli-cell only syndrome #2
Data processing Scan images were converted to raw values by the CodeLink Expression analysis software (GE Healthcare, USA) and these normalized by quantile normalization using the Bioconducter package 'affy'.
 
Submission date Apr 30, 2010
Last update date Apr 30, 2010
Contact name Andrej-Nikolai Spiess
E-mail(s) a.spiess@uke.uni-hamburg.de
Phone +49-40-42803-1585
Fax +49-40-42803-1554
URL http://www.dr-spiess.de
Organization name University Hospital Hamburg-Eppendorf
Department Andrology
Lab Molecular Andrology
Street address Martinistr. 52
City 20246 Hamburg
State/province n/a
ZIP/Postal code n/a
Country Germany
 
Platform ID GPL2891
Series (1)
GSE21613 Analysis of testicular transcriptome changes in the presence of Y-chromosomal microdeletions

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
109 7.09929408
110 7.941311311
111 9.582853154
112 9.959028183
113 11.40963405
114 8.217974663
116 9.322407511
117 9.31379605
118 7.217566476
119 7.568509613
120 7.785376222
121 7.421157652
123 7.598520725
124 9.821385387
125 10.2823709
126 6.42448749
127 8.417139332
128 10.3703584
130 11.2983027
131 9.390872905

Total number of rows: 20469

Table truncated, full table size 348 Kbytes.




Supplementary file Size Download File type/resource
GSM539525.txt.gz 2.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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