|
| Status |
Public on Jan 10, 2020 |
| Title |
mDC_HIVpositive Donor 2_ARV_replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood myeloid dendritic cells
|
| Organism |
Homo sapiens |
| Characteristics |
donor hiv status: HIVpositive Donor 2
donor hiv treatment status: ARV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Myeloid dendritic cell were isolated by flow cytometry and treated with RLT Buffer (Qiagen) for cell lysis. RNA was extracted from using the RNeasy Micro kit (Qiagen), according to the manufacturer’s protocol. RNA quality control was performed using a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) and Experion automated electrophoresis system (Bio-Rad Laboratories).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp II kit for Illumina arrays.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
technical replicate: 2
|
| Data processing |
The data were normalized using quantile normalization in R using Bioconductor as described in Caskey et al., 2011. Batch correction was performed with ComBat. Technical replicates were averaged in the matrix normalized data to yield the expression values used for the subsequent analysis.
|
| |
|
| Submission date |
Oct 29, 2019 |
| Last update date |
Jan 10, 2020 |
| Contact name |
Shannon Murray |
| E-mail(s) |
smurray1@uw.edu
|
| Phone |
(954) 560-0798
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Street address |
1100 Fairview Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE139559 |
Myeloid Dendritic Cells from People Living with HIV have Altered Gene Expression Not Restored by Anti-Retroviral Therapy |
|
