|
| Status |
Public on Jan 12, 2022 |
| Title |
WholeBlood_HVTN087132520201_Day3 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral Blood, PaxGene
|
| Organism |
Homo sapiens |
| Characteristics |
participant: HVTN087132520201
gender: male
age: 44y
race: black or african american
ethnicity: not hispanic or latino
group: 1E
vaccinations received: D---
treatment: NONE
day: 3
tissue: whole blood
|
| Treatment protocol |
Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.
|
| Scan protocol |
Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth
|
| Description |
Whole blood gene expression of participant HVTN087132520201 on day 3 after treatment: NONE
|
| Data processing |
The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.
|
| |
|
| Submission date |
Jan 13, 2019 |
| Last update date |
Jan 12, 2022 |
| Contact name |
David Lewis |
| E-mail(s) |
djmlewis@hotmail.com
|
| Organization name |
Imperial College London
|
| Department |
ICRF
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21272 |
| Series (1) |
| GSE125019 |
Gene expression signatures after immunisation with an HIV-1 recombinant Vesicular Stomatitis Virus (VSV) vaccine following three priming doses of IL-12 pDNA enhanced HIV-1 multi-antigen pDNA vaccine (BIOVACSAFE protocol HVTN087) |
|
