|
| Status |
Public on Aug 20, 2009 |
| Title |
splenocytes_62%_d11_2 |
| Sample type |
RNA |
| |
|
| Source name |
62% CD45 splenocytes 11 days post- EBOV-infection
|
| Organism |
Mus musculus |
| Characteristics |
mice strain: C57BL/6 CD45+/- (PTPRC+/-)
tissue: Splenocytes
pathogen: Mouse adapted Ebola Zaire
route of pathogen infection: Intraperitoneal
pathogen load: 1000 pfu
|
| Biomaterial provider |
Rekha Panchal
|
| Treatment protocol |
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 11 days post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were homogenized in 3mL of TRIzol. The homogenate was extracted with 1.2 mL of Chloroform. Eppendorf PLG tubes were used to aid in phase separation. The aqueous phase was removed and processed for RNA using the Qiagen RNease Mini kit according to manufacturer’s instruction (DNase Treatment protocol). RNA was eluted in 40 uL of RNase-free water. RNA concentrations were determined using A260 values obtained from the SpectraMax Plus plate reader spectrophotometer. RNA RIN values were determined by analysis on the Agilent Bioanalyzer (RNA 6000 Nano kit).
|
| Label |
biotin
|
| Label protocol |
2 ug of DNA was labeled with biotin using the Affymetrix GeneChip® IVT kit according to manufacturer’s instruction.
|
| |
|
| Hybridization protocol |
The biotin labeled RNA was hybridized 16-24 hours at 45 degrees Celsius at 60RPM to Affymetrix Mouse Genome 430 2.0 according to manufacturer’s instruction. Following hybridization, the GeneChip® Fluidics Station 450 was used for the wash and stain operation of Affymetrix Mouse GeneChip® arrays. Fluidic protocol EukGE-Ws2v5_450 was used.
|
| Scan protocol |
The processed Affymetrix Mouse GeneChip® array was scanned on the GeneChip® Scanner 3000 7G according to manufacturer’s instruction.
|
| Description |
CD45 62% (C57BL/6) mouse splenocytes 11 days post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.
|
| Data processing |
Data were preprocessed and summarized in R/Bioconductor using GC-RMA.
|
| |
|
| Submission date |
Aug 04, 2009 |
| Last update date |
Aug 06, 2009 |
| Contact name |
Brian D. Peyser |
| Organization name |
USAMRIID
|
| Department |
Bacteriology
|
| Lab |
Sina Bavari PhD
|
| Street address |
1425 Porter St
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE17509 |
Reduced levels of protein tyrosine phosphatase CD45 protect mice from the lethal effects of Ebola virus infection |
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