|
| Status |
Public on Nov 01, 2016 |
| Title |
Hippocampus_HSV-1_10^3_647_vs_Control_555_rep 1_2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Hippocampus_Vero cell control
|
| Organism |
Mus musculus |
| Characteristics |
strain: SJL/J
infected with: Vero cell suspension (control)
tissue: brain_Hippocampus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the RNAqueous-Micro Kit (Life Technologies) following manufacturer's instructions.
|
| Label |
AlexaFluor 555
|
| Label protocol |
Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Ambion) following manufacturer's instructions. Upon 2 rounds of amplification, each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
Hippocampus_HSV-1_10^3 plaque forming units
|
| Organism |
Mus musculus |
| Characteristics |
strain: SJL/J
tissue: brain_Hippocampus
infected with: HSV-1 10^3 pfu
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the RNAqueous-Micro Kit (Life Technologies) following manufacturer's instructions.
|
| Label |
AlexaFluor 647
|
| Label protocol |
Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Ambion) following manufacturer's instructions. Upon 2 rounds of amplification, each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Hybridization and washing was performed according to the Two-Color Microarray-Based Gene Expression Analysis protocol for a 4x44K microarray format (Agilent technologies) following manufacturer's instructions.
|
| Scan protocol |
Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3) following the scan settings for a 4x44K microarray format according to manufacturer's instructions.
|
| Data processing |
The .TIFF images were uploaded into Feature Extraction (Agilent technologies, G2567AA FE software, v.10.5), the spots were identified, and the grids constructed using the GE2-v5_95_Feb07 & GE2_105_Dec08 protocol and the 014868_D_20060807 grid file for the whole mouse genome 4x44K expression arrays which were downloaded from the Agilent technologies website. Background calculations were performed by the feature extraction software using spatial and multiplicative detrending and normalization was performed using linear and lowess. The p-value to determine differential expression was 0.01 and the resulting log10 ratios from the feature extraction software were provided as the red (AlexaFlour 647)/green (AlexaFlour 555) channel.
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
Nov 01, 2016 |
| Contact name |
Stephanie A Booth |
| E-mail(s) |
Stephanie.Booth@phac-aspc.gc.ca
|
| Organization name |
Public Health Agency of Canada
|
| Department |
Molecular PathoBiology
|
| Street address |
1015 Arlington Street
|
| City |
Winnipeg |
| State/province |
Manitoba |
| ZIP/Postal code |
R3E 3R2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE51040 |
Host miRNA molecular signatures in the brains of mice are associated with acute herpes simplex virus 1 encephalitis |
|
