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Sample GSM389676 Query DataSets for GSM389676
Status Public on Nov 28, 2013
Title non-CF subject 37
Sample type RNA
 
Source name rectal suction specimens
Organism Homo sapiens
Characteristics tissue: rectal mucosal epithelia
genotype: non-CF
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from rectal suction biopsies of CF patients and non-CF individuals using the RNAeasy mini kit (Qiagen, Hilden, D). Quality of total RNA was monitored by gel electorphoresis.
Label biotin
Label protocol Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT-T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo). For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).
 
Hybridization protocol The Human GeneChip HG-U133A was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite version 5.0.
Scan protocol standard Affymetrix protocol
Description experimental design: Collect rectal mucosal epithelia by suction biopsy from CF-patients, homocygous for the CFTR D508 mutation and from non CF-individuals; monitor activity of mucosal epithelia by ICM; analysis of gene expression profiles.
Data processing Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data were normalized using a rank based normalization algorithm (rank mean) in MatLab.
 
Submission date Apr 06, 2009
Last update date Nov 28, 2013
Contact name Stefan Wolfl
E-mail(s) wolfl@uni-hd.de
Organization name Heidelberg University, Heidelberg, Germany
Department Institute of Pharmacy and Molecular Biotechnology
Lab Pharm. Biology and Bioanalytics
Street address Im Neuenheimer Feld 364
City Heidelberg
ZIP/Postal code D-69120
Country Germany
 
Platform ID GPL96
Series (1)
GSE15568 Gene expression in rectal epithelia of cystic fibrosis patients

Data table header descriptions
ID_REF
VALUE Signal intensity obtained after rank based normalization (rank mean) of primary data obtained by default analysis using MAS 5.0.

Data table
ID_REF VALUE
AFFX-BioB-5_at 1925.72
AFFX-BioB-M_at 3008.04
AFFX-BioB-3_at 1480.28
AFFX-BioC-5_at 3149.61
AFFX-BioC-3_at 3674.27
AFFX-BioDn-5_at 3658.89
AFFX-BioDn-3_at 19107.46
AFFX-CreX-5_at 28134.50
AFFX-CreX-3_at 38597.66
AFFX-DapX-5_at 11.50
AFFX-DapX-M_at 13.33
AFFX-DapX-3_at 15.66
AFFX-LysX-5_at 136.09
AFFX-LysX-M_at 24.17
AFFX-LysX-3_at 16.13
AFFX-PheX-5_at 15.79
AFFX-PheX-M_at 27.79
AFFX-PheX-3_at 116.94
AFFX-ThrX-5_at 26.45
AFFX-ThrX-M_at 29.54

Total number of rows: 22283

Table truncated, full table size 387 Kbytes.




Supplementary file Size Download File type/resource
GSM389676.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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