|
| Status |
Public on Dec 05, 2012 |
| Title |
CD16 vs CDH16 (dye swap reps) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
CD16
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+CD8- cells from pooled plasma
infection: untreated
time (days post-infection): 16
|
| Treatment protocol |
untreated versus infected by HIV-1 at MOI=0.01, RNA was extracted at different days post infection
|
| Growth protocol |
Cultured in ActiCyte -TC media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNA STAT-60
|
| Label |
Hy3, Hy5
|
| Label protocol |
The samples were labeled using the miRCURY™ Hy3™/Hy5™ power labeling kit
|
| |
|
| Channel 2 |
| Source name |
CDH16
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+CD8- cells from pooled plasma
infection: HIV1 infected
time (days post-infection): 16
|
| Treatment protocol |
untreated versus infected by HIV-1 at MOI=0.01, RNA was extracted at different days post infection
|
| Growth protocol |
Cultured in ActiCyte -TC media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNA STAT-60
|
| Label |
Hy3, Hy5
|
| Label protocol |
The samples were labeled using the miRCURY™ Hy3™/Hy5™ power labeling kit
|
| |
|
| |
| Hybridization protocol |
The samples were hybridized on the miRCURY™ LNA Array (v.9.2) as per Exiqons protocols.
|
| Scan protocol |
Arrays were scanned by Agilent Scanner as per Agilent's default protocol
|
| Description |
Infected vs. control at day 16
Infected vs. control dye Swap at day 16
US45102989_13730770_S01_crop_Exiqon_KBB3.txt: CD16_Hy3vsCDH16_Hy5
US45102989_13730771_S01_crop_Exiqon_KBB3.txt: CDH16_Hy3vsCD16_Hy5
|
| Data processing |
When the array was scanned, a GAL file specially designed for human was provided by the manufacturer and it was used to extract intensities from the array. The GAL file does not have any spots other than human miRNAs. Therefore, the non-human miRNAs (not useful for this study) are never reported by the scanner.
Log ratios between the Hy3/Hy5 have been provided along with the normalized independent Hy3 and Hy5 signals. The quantified signals (background correction) were normalized using the global Lowess method.
LOWESS normalized log ratio (infected/untreated) using Limma package. When dye swap is present, it is the mean of the two replicates.
|
| |
|
| Submission date |
Dec 05, 2012 |
| Last update date |
Dec 05, 2012 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL7724 |
| Series (1) |
| GSE42737 |
Interplay between HIV-1 infection and host microRNAs |
|
