Total RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer’s protocol
Label
biotin
Label protocol
Amplified and biotin-labeled RNAs were obtained from 2µg of total RNA, by a round of in vitro transcription (dIVT) using the Message Amp a RNA kit version II (Ambion), following the manufacturer’s protocol.
Hybridization protocol
10 µg of biotin-labeled RNA were fragmented using 5 µl fragmentation buffer in a final volume of 20 µl, then mixed with 240 µl Amersham hybridization solution and injected onto Codelink Uniset Human Whole Genome bioarrays. Arrays were hybridized overnight at 37°C, then washed in stringent TNT buffer at 46°C for 1 h before performing a streptavidin-cy5 detection step. Each array was incubated for 30 min in 3,4 ml streptavidin-cy5 solution, washed four times in 240 ml TNT buffer, rinsed twice in 240 ml water containing 0.2M Triton X-100, and then, dried by centrifugation at 650g.
Scan protocol
Arrays were then scanned at 635nm using an Axon Genepix 4000B Scanner (Axon).
Data processing
Data extraction and raw data normalization were performed using the CodeLink Gene Expression Analysis v4.0 software. Normalization was performed by the global method. The threshold was calculated using the normalized signal intensity of the negative controls supplemented by 3 times the standard deviation. Spots with signal intensity below this threshold were referred to as “absent”.
Analysis of the early transcriptome signature of infection of primary endothelial cells by Nipah virus vs. Nipah virus deleted for the expression of non-structural C protein
Data table header descriptions
ID_REF
SIGNAL_RAW
The spot density, which is the difference between the spot mean and the local background median.
VALUE
The normalized intensity value (the raw intensity divided by the normalization factor)
Quality_flag
The metrics used to indicate the quality of a spot: G - The spot has passed all quality control measures and is defined as good. C, I, L, M, and S indicate presence of issues.
