|
| Status |
Public on May 29, 2016 |
| Title |
pre-vaccination blood sample from donor M935 |
| Sample type |
RNA |
| |
|
| Source name |
Blood sample from donor M935
|
| Organism |
Macaca mulatta |
| Characteristics |
donor: M935
vaccination group: ALVAC-SIV/gp120/MF59
vaccination time: pre-vaccination
time after immunization: pre
number of siv challenge to infection: 3
tissue: Blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using Agencourt RNAdvance Blood Kit. The isolated total RNA was checked for quantity and quality 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 |
P162_M935_prevax
pre-vaccination blood transcriptional profilling
|
| Data processing |
Raw probe intensities were preprocessed using the R (version 3.2.1) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.42.0). Log2 transformation was performed for variance stabilisation and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.24.15).
|
| |
|
| Submission date |
Sep 02, 2015 |
| Last update date |
May 29, 2016 |
| 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 (1) |
| GSE72624 |
Transcriptomic profiling of rhesus macaques vaccinated with ALVAC-SIV/gp120 adjuvanted in Alum or MF59. |
|
