|
| Status |
Public on Dec 31, 2016 |
| Title |
EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D3_3 |
| Sample type |
RNA |
| |
|
| Source name |
EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D3_3
|
| Organism |
Mus musculus |
| Characteristics |
run_folder: Microarray
run_rowid: 60312
|
| Treatment protocol |
Mice were infected by intraperitoneal (i.p.) injection with 100 focus-forming units (ffu) of either MA-ZEBOV or WT ZEBOV diluted in 0.2 ml of Dulbecco’s minimum essential medium (DMEM). Mock-infected mice were i.p. inoculated with DMEM alone. Mice were humanely euthanized on days 3 and 5 post-infection, and spleens and livers removed and incubated in RNAlater (Qiagen, Valencia, CA). Tissues were then homogenized in Trizol reagent (ThermoFisher Scientific, Waltham, MA) to both inactivate virus and stabilize RNA, and stored at -80 C until RNA extraction.
|
| Growth protocol |
Six to nine week-old male mice (C57Bl/6J, MAVS-/-) were used in all experiments. Mice were housed in microisolator cages and allowed to acclimatize to the BSL4 environment for a least 5 days prior to use in experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from mouse spleens and livers using a Qiagen RNeasy Minikit with RNAlater solution (Qiagen, Valencia, CA) according to the manufacturer's instructions. RNA was further purified using RNeasy columns (Qiagen, Valencia, CA). RNA samples were spectroscopically verified for purity, and the quality of the intact RNA was assessed using an Agilent 2100 Bioanalyzer. For each set of treatment conditions, three of the five RNA samples exhibiting the highest RNA integrity number (RIN) determined using the Bioanalyzer were used for microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
cRNA probes were generated from each sample by the use of an Agilent one-color LowInput Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA).
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| |
|
| Hybridization protocol |
). Individual cRNA samples were hybridized to Agilent mouse whole-genome oligonucleotide 4-by-44 microarrays (approximately 39,000 unique mouse genes) according to the manufacturer's instructions. To enable examination of animal-to-animal variation as part of the data analysis, samples from individual animals were not pooled; included were samples from three animals per time point for each virus (60 animals total). Select samples were hybridized a second time (n = 2 technical replicates) to verify the quality of the process.
|
| Scan protocol |
Slides were scanned with an Agilent DNA microarray scanner, and the resulting images were analyzed using Agilent Feature Extractor version 8.1.1.1. This software was used to perform image analysis, including significance of signal and spatial detrending and to apply a universal error model. For these hybridizations, the most conservative error model was applied.
|
| Data processing |
standard Agilent protocol
|
| |
|
| Submission date |
Jun 13, 2016 |
| Last update date |
Dec 31, 2016 |
| Contact name |
Angela Rasmussen |
| E-mail(s) |
alr2105@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Center for Infection and Immunity
|
| Street address |
722 W. 168th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21810 |
| Series (1) |
| GSE83309 |
A systems approach reveals MAVS signaling in myeloid cells as critical in resistance to Ebola virus in murine models of infection |
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