|
| Status |
Public on Feb 15, 2019 |
| Title |
pre-vaccination blood sample from donor 615235 stimulated 15 hours with DMSO |
| Sample type |
RNA |
| |
|
| Source name |
Blood sample from donor 615235
|
| Organism |
Homo sapiens |
| Characteristics |
donor: 615235
post-thraw resting: no
rna extraction protocol: Micro kit
stimulation: DMSO
stimulation time: 15
stimulation time unit: hours
visit: pre
hiv infection: No
|
| Treatment protocol |
Peripheral blood mononuclear cells were stimulated in vitro for 15 hours with short peptides (15-mers) of HIV-1 Env or for 15 hours with the vehicle (DMSO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Rneasy micro kit (Qiagen) and the quality of the RNA was confirmed using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.
|
| |
|
| Hybridization protocol |
Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.
|
| Scan protocol |
The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).
|
| Description |
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d615235_pre_DMSO_15h
|
| Data processing |
Raw probe intensities were preprocessed using the R (version 3.3.2) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.48.0). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.30.7).
|
| |
|
| Submission date |
Sep 10, 2017 |
| Last update date |
Feb 17, 2019 |
| Contact name |
Slim Fourati |
| E-mail(s) |
slim.fourati@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Medicine
|
| Lab |
Fourati
|
| Street address |
300 E Superior St
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE103671 |
Transcriptomic profiling of RV144 trial participants before and after vaccination with ALVAC-HIV and AIDSVAX B/E.[rv144pilot] |
| GSE103740 |
Transcriptomic profiling of RV144 trial participants |
|
