|
| Status |
Public on Nov 12, 2007 |
| Title |
CD45-negative nSP cell fraction, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse CD45-/nSP cells isolated via SP sorting
|
| Organism |
Mus musculus |
| Characteristics |
Adult, male, C57Bl/6
|
| Treatment protocol |
Mice were sacrificed at 8-10 weeks of age, and the jejunum was harvested. Mucosal digests were prepared using collagenase and dispase. These were then subject to SP sorting via Hoechst 33342 dye exclusion. Cells were also stained with fluorescein isothiocyanate (FITC) labeled anti-CD45 antibody (BD Pharmingen, San Diego, CA) to eliminate bone-marrow derived cells from the populations to be analyzed. Propidium iodide (PI) was used to exclude dead cells.
|
| Growth protocol |
All mice for this study were housed in our animal facility under a 12-hour light/dark cycle, and all had unrestricted access to rodent Lab Chow #5001 (PMI Nutrition International, Brentwood, MO) as well as acidified tap water. The Institutional Animal Care and Use Committee of Baylor College of Medicine approved all experimental procedures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted using an RNeasy Mini Kit (Qiagen, Valencia, CA) per the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
50 ng of total RNA was amplified using the Affymetrix Two Cycle Target Labeling Kit according to standard Affymetrix protocols (Expression Analysis Technical Manual, 2004, Affymetrix). Biotinylated cRNA were prepared from 5 mcg of total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 mcg of biotinylated cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix Mouse Genome 430 2.0 GeneChips. GeneChips were washed and stained using the Affymetrix Fluidics station 400 according to standard Affymetirx protocols.
|
| Scan protocol |
Laser scanning of the chips was performed using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from mouse CD45-/nSP cells isolated via SP sorting
|
| Data processing |
The data were analyzed using the dChip software platform (v2005).
|
| |
|
| Submission date |
Sep 11, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Ajay S Gulati |
| E-mail(s) |
ajay_gulati@med.unc.edu
|
| Phone |
(919) 966-7886
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Pediatric Gastroenterology
|
| Street address |
130 Mason Farm Road, CD#7220
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE9013 |
Expression data from side-population sorted putative intestinal stem cells. |
|
| Relations |
| Reanalyzed by |
GSE119085 |
