|
| Status |
Public on Jan 29, 2010 |
| Title |
Hnf1-CDX2rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
HIEC pTetON + DOX
|
| Organism |
Homo sapiens |
| Characteristics |
HIEC stably infected with pTetON plasmid (Clontech)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from reference pool was isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp 1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)
|
| Label |
Cy3
|
| Label protocol |
aRNA amplified using TargetAmp 1-round aRNA amplification kit 103 following manufacturer's instructions (Epicentre Biotechnologies, Madison, WI)
1 µg of aRNA was primed with 3 µl of 2 µg/µL hexamer random primers at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, 200µM dTTP and 300µM aa-dUTP.
|
| |
|
| Channel 2 |
| Source name |
HIEC-pRevTRE-Hnf1/CDX2
|
| Organism |
Homo sapiens |
| Characteristics |
HIEC pTetON stably infected with pRevTRE-Hnf1 and pRevTRE-CDX2
|
| Treatment protocol |
treated with doxycycline for 30 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from HIEC pTetON stably infected with pRevTRE-Hnf1 and pRevTRE-CDX2 treated with DOX was isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)
|
| Label |
Cy5
|
| Label protocol |
aRNA amplified using TargetAmp 1-round aRNA amplification kit 103 following manufacturer's instructions (Epicentre Biotechnologies, Madison, WI)
1 µg of aRNA was primed with 3 µl of 2 µg/µL hexamer random primers at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, 200µM dTTP and 300µM aa-dUTP.
|
| |
|
| |
| Hybridization protocol |
Arabidopsis cDNA and hybridization buffer (formamide 50%, SSC 5X, SDS 0.1%) were added, and samples were applied to microarrays enclosed in hybridization chambers overnight at 42°C. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an ScanArray Express (Packard Bioscience).
|
| Description |
HIEC expressing Hnf1 and CDX2: Biological replicate 3
|
| Data processing |
Images were quantified using Spotfinder 3 Software (The Institute for Genomic Research: www.tigr.org). Then LOWESS normalized, background subtracted data were obtained from log2 of processed Red signal/processed Green signal. TIGR package software was used.
|
| |
|
| Submission date |
May 12, 2008 |
| Last update date |
Jan 29, 2010 |
| Contact name |
Jean-François Beaulieu |
| E-mail(s) |
Jean-Francois.Beaulieu@Usherbrooke.ca
|
| Organization name |
Université de Sherbrooke
|
| Department |
Anatomie & biologie cellulaire
|
| Street address |
3001, 12ème avenue nord
|
| City |
Sherbrooke |
| State/province |
Québec |
| ZIP/Postal code |
J1H 5N4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6854 |
| Series (1) |
| GSE11421 |
HNF-1alpha Triggers Initiation of the Human Intestinal Cell Differentiation Program in Cooperation with Cdx-2 and GATA-4 |
|
