|
| Status |
Public on Aug 27, 2015 |
| Title |
control kidney 475 |
| Sample type |
RNA |
| |
|
| Source name |
Donor kidney from a BALB/c mouse latently infected with MCMV
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Control Kidney
age: 48 hours post transplant
strain: BALB/c
|
| Treatment protocol |
Donor kidneys from latently infected BALB/c mice were transplanted into recipient C57BL/6 mice as previously described (Zhang et al., 1995), except that recipients were bi-laterally nephrectomized at the time of the transplant. The pararenal glands were left intact. The contralateral donor kidney was frozen in liquid nitrogen at the time of the transplant for use as a matching, Day 0 latent control. Transplanted kidneys were frozen in liquid nitrogen at the time of sacrifice.
|
| Growth protocol |
BALB/c and C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor, ME). MCMV (Smith strain) was purchased from the American Type Culture Collection (Manassas, VA), and propagated in mice by harvesting salivary glands 14 days post-infection. Virus stocks were titered on confluent monolayers of murine embryo fibroblasts. To establish latency, three to four-week old female BALB/c mice were infected i.p. with 5 x 105 pfu of MCMV (Smith strain) and housed for 3-6 months in the Northwestern University Center for Comparative Medicine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissue collected at 48 hr post-transplant was immediately transferred to tubes containing TriZol and 5 mm stainless steel beads (Qiagen), and the tissue was disrupted by mechanical shaking in a TissueLyser (Qiagen) at room temperature for 5 min. RNAs were purified with PureLink RNA Minikits (Ambion), using on-column DNAse treatment as directed by the manufacturer. RNA was quantified on a nanodrop spectrophotometer, and quality was assessed on an Agilent 2100 bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 2.1 ST ArrayArray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
matching kidney control replicate from mouse 475
|
| Data processing |
The data were analyzed with Partek Genomics Suite 6.6 using Robubst Multiarray Average (RMA) algorithm with quantile normalization method.
|
| |
|
| Submission date |
Aug 26, 2015 |
| Last update date |
Aug 27, 2015 |
| Contact name |
Chunfa Jie |
| E-mail(s) |
cjie.jhmi@gmail.com
|
| Phone |
3124043831
|
| Organization name |
Des Moines University
|
| Street address |
3200 Grand Ave
|
| City |
Des Moines |
| State/province |
IA |
| ZIP/Postal code |
50266 |
| Country |
USA |
| |
|
| Platform ID |
GPL17400 |
| Series (1) |
| GSE72392 |
Kidney gene expression profile following the transplant-induced reactivation of MCMV |
|
