|
| Status |
Public on Dec 08, 2006 |
| Title |
Klf9KO_jejunum_PND30_3 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse jejunum, PND30
|
| Organism |
Mus musculus |
| Characteristics |
Klf9 mutant (Klf9KO) mice jejunum; Age: PND 30
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
|
| Label |
Biotin
|
| Label protocol |
8 ug total RNA was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
|
| |
|
| Hybridization protocol |
10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) mouse 430A GeneChip (5 chips per genotype group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
|
| Scan protocol |
GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
|
| Description |
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Data processing |
To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500
|
| |
|
| Submission date |
Dec 04, 2006 |
| Last update date |
Dec 07, 2006 |
| Contact name |
Rijin Xiao |
| E-mail(s) |
[email protected]
|
| Phone |
501-364-2790
|
| Fax |
501-364-3161
|
| Organization name |
Nutrition Center, Arkansas Chidren's Hospital
|
| Street address |
2020 Marshall Street
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72202 |
| Country |
USA |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE6443 |
Intestinal crypt stem and transit cell proliferation and villus cell migration in mice lacking Klf9 |
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