Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 359
Release date: Mar 3 2018
Last update date: Aug 13 2018
Access: Public
Diseases: Coinfection
Dataset link Progression of whole blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in patients with severe influenza

Experimental Protocol


At each time point, 3 ml of whole blood were collected into each of two Tempus tubes (Applied Biosystems/Ambion) by trained research staff following a standard phlebotomy protocol. Blood was vigorously mixed immediately following collection and stored at -80°C before RNA extraction. For each patient, the contents of one tube were used for analysis and the other tube was retained in case of assay failure. RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion), as per the manufacturer’s instructions. 250 ug of isolated total RNA was globin-reduced using the GLOBINclear 96-well format kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions. Total and globin-reduced RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA yield was assessed using a NanoDrop8000 spectrophotometer (NanoDrop Products, Thermo Fisher Scientific). High-quality (>6.5 RIN) whole blood RNA was successfully obtained and processed by microarray in all cases. Biotinylated, amplified antisense complementary RNA (cRNA) targets were prepared from 200-250 ng of globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion). For each sample, seven hundred and fifty nanograms of labelled cRNA were hybridised overnight to Illumina Human HT12 V4 BeadChip arrays (Illumina), which contained greater than 47,000 probes. The arrays were washed, blocked, stained and scanned on an Illumina iScan, as per the manufacturer’s instructions. GenomeStudio (Illumina) was used to perform quality control and generate signal intensity values. Contributor: the MOSAIC Investigators

Repositories


GEO

GSE111368

BioProject

PRJNA436726

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Contact


Long Hoang