|
| Status |
Public on Nov 08, 2013 |
| Title |
HSC,WT,rep4 |
| Sample type |
RNA |
| |
|
| Source name |
hematopoietic stem cells, wild-type mouse
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild-type Ahr
genetic background: C57BL/6J
cell type: hematopoietic stem cells
|
| Growth protocol |
Mice were weaned at 3 weeks and fed ad libitum thereafter.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were killed by carbon dioxide inhalationat 8 weeks of age. Bone marrow was depleted of Lin+ cells as described by Singh et al. 2009 (Carcinogenesis 30;11-19). SLAM+ HSC were extracted from Lin- cells as described by Kiel et al. 2005 (Cell 121;1109-1121). Selected cells were collected in RNAlater reagent (Ambion) and frozen at -80C until total RNA was extracted with a Micro RNeasy kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA was prepared from total RNA with the Nugen WT-Ovation PicoSL Kit.
|
| |
|
| Hybridization protocol |
Arrays were hybridized overnight with 2.8 ug cDNA using using an Affymetrix hyb station, with hybridization solutions and conditions recommended by the kit manufacturer (Nugen).
|
| Scan protocol |
After arrays were washed they were stained with phycoerythrin-streptavidin as recommended by Affymetrix (including anti-SAPE antibody enhancement), and phycoerythrin fluorescence was determined with an Affymetrix scanner. Affymetrix Cammand Console software was used to control the scanner and generate raw image files (DAT) and to consolidate data from individual pixels into array features (CEL files).
|
| Data processing |
CEL files were quantile normalized and background subtracted with the Iterplier algorithm of Affymetrix Expression Console.
|
| |
|
| Submission date |
May 15, 2013 |
| Last update date |
Nov 10, 2013 |
| Contact name |
Stephen Welle |
| E-mail(s) |
swelle@rochester.rr.com
|
| Organization name |
University of Rochester
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE46976 |
Effect of aryl hydrocarbon receptor (Ahr) gene knockout on expression profiles of murine hematopoietic stem cells |
|
