|
| Status |
Public on Jan 06, 2020 |
| Title |
wholeblood__CRC305E92633_0h |
| Sample type |
RNA |
| |
|
| Source name |
whole blood,PaxGene
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: CRC305E
treatment: PLACEBOE
day: 0
hour: 0
tissue: whole blood
participant: CRC305E92633
gender: male
age: 21y
race: white
ethnicity: not hispanic or latino
|
| Treatment protocol |
Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA extracted from the whole blood in PaxGene tubes or the muscle biopsies stored in RNAlater 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 |
600ng 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 CRC305E92633 at 0 hours post immunization
|
| 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.
Quantile normalized signal intensity using limma 3.38.3, read.maimages source = agilent, backgroundCorrect method= normexp, normalizeBetweenArrays method= quantile
|
| |
|
| Submission date |
Jan 07, 2019 |
| Last update date |
Jan 07, 2020 |
| 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) |
| GSE124719 |
Gene expression signatures in blood and muscle biopsy after intramuscular immunization of healthy adult humans with adjuvanted vaccines (BIOVACSAFE protocol 305E) |
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