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Status |
Public on Feb 15, 2019 |
Title |
pre-vaccination blood sample from donor 611459 stimulated 15 hours with 92TH023ENV |
Sample type |
RNA |
|
|
Source name |
Blood sample from donor 611459
|
Organism |
Homo sapiens |
Characteristics |
donor: 611459 post-thraw resting: no rna extraction protocol: Micro kit stimulation: 92TH023ENV 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.
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|
|
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 92TH023ENV RV144_d611459_pre_92TH023ENV_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).
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|
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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 |
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