|
| 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 |
|
