|
| Status |
Public on Oct 18, 2013 |
| Title |
BRAIN|ORF73|SC017 |
| Sample type |
RNA |
| |
|
| Source name |
ORF73
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
tissue: BRAIN
infectious agent: ORF73.stop
|
| Treatment protocol |
After cardiac perfusion with PBS, brains, livers and spleens were harvested at 28 days post infection (dpi) and immediately snap frozen.
|
| Growth protocol |
7-9 week old male C57BL/6J mice were infected intranasally with wild-type (WT) MHV68, ORF73.stop mutant virus or mockulum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the ToTALLY RNA kit (Ambion) from tissues incubated in RNAlater-ICE (Ambion) and purified by lithium chloride precipitation and RNeasy column. Equal amounts of RNA were pooled from three to four mice per condition for each microarray chip.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug (samples 16xxx) or 100 ng (samples 21xxx) total RNA (Expression Analysis Technical Manual, 2008, Affymetrix). RNA was labeled at the Multiplexed Gene Analysis Core Facility at Washington University in St. Louis.
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug (samples 16xxx) or 12.5 ug (samples 21xxx) of cRNA were hybridized for 16 hr at 45C on Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.
|
| Description |
mice harvested midday
|
| Data processing |
The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings and global scaling as normalization method. Target intensity of arrays was set to 1500 (for samples 16xxx) or 100 (for samples 21xxx). Data were normalized using Robust Multi-array Average normalization routine in Affymetrix’s Expression Console software.
|
| |
|
| Submission date |
Oct 17, 2013 |
| Last update date |
Oct 18, 2013 |
| Contact name |
Ramnik J Xavier |
| E-mail(s) |
xavier@molbio.mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE51365 |
Latent gammaherpesvirus 68 infection induces distinct transcriptional changes in different organs |
|
