|
| Status |
Public on Mar 22, 2016 |
| Title |
STI KO_WNV_Brain_CD45+ cells 1 |
| Sample type |
RNA |
| |
|
| Source name |
STI KO_Brain_day 10 post infection
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: STI knockout
infected with: 100 PFU West Nile Virus (WNV)
time point: day 10 p.i
tissue: Brain
cell type: CD45+ cells
|
| Treatment protocol |
Mice were infected with 100 PFU WNV s.c. Brains were harvested at day 10 p.i. CD45+ cells from brains were isolated for microarray analysis.
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| 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 |
RNA for the microarray was processed using a NuGEN WT-Ovation Pico RNA Amplification System together with a NuGEN WT-Ovation Exon Module. Samples were hybridized and loaded onto Affymetrix Mouse gene 2.0. Arrays
|
| Scan protocol |
scanned with a HiScan bead array system, and data were collected using GeneChip Operating Software
|
| Data processing |
Data from Affymetrix Mouse gene 2.0 Expression BeadChip were normalized and median polished using Robust Multichip Average background correction with log2-adjusted values. After obtaining the log2 expression values for genes, significance testing was performed comparing the two groups (CD45+ cells from brains of WT and IPS-1-/- mice). Significance of expression differences was assessed using a false discovery rate (FDR) cutoff of 0.05 and a twofold change. Analysis and visualization of data and pathway analysis were performed using PartekGS software and Ingenuity Pathway Analysis software.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46
|
| |
|
| Submission date |
Mar 21, 2016 |
| Last update date |
Mar 22, 2016 |
| Contact name |
Rahul Vijay |
| E-mail(s) |
rahul-vijay@uiowa.edu
|
| Phone |
3193357576
|
| Organization name |
University of Iowa
|
| Department |
Microbiology and Immunology
|
| Lab |
Butler Lab
|
| Street address |
51 Newton Road
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE79417 |
Expression data of Brain CD45+ cells from WT and STI knockout mice after WNV infection |
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