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Sample GSM389655 Query DataSets for GSM389655
Status Public on Nov 28, 2013
Title CF (D508) subject4
Sample type RNA
 
Source name rectal suction specimens
Organism Homo sapiens
Characteristics tissue: rectal mucosal epithelia
genotype: CFTR D508
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 1470.91
AFFX-BioB-M_at 3958.05
AFFX-BioB-3_at 1724.85
AFFX-BioC-5_at 4359.88
AFFX-BioC-3_at 3782.42
AFFX-BioDn-5_at 2981.52
AFFX-BioDn-3_at 18813.77
AFFX-CreX-5_at 32127.74
AFFX-CreX-3_at 44445.66
AFFX-DapX-5_at 9.07
AFFX-DapX-M_at 165.46
AFFX-DapX-3_at 16.55
AFFX-LysX-5_at 158.35
AFFX-LysX-M_at 157.48
AFFX-LysX-3_at 27.22
AFFX-PheX-5_at 8.13
AFFX-PheX-M_at 20.00
AFFX-PheX-3_at 119.71
AFFX-ThrX-5_at 40.29
AFFX-ThrX-M_at 91.13

Total number of rows: 22283

Table truncated, full table size 387 Kbytes.




Supplementary file Size Download File type/resource
GSM389655.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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