Illumina HiSeq 4000 paired end sequencing; GSM2886136: Leicester_non_progressor_longitudnal_only_Sample2; Homo sapiens; RNA-Seq

Leicester_non_progressor_longitudnal_only_Sample2

Whole blood transcriptional signatures distinguishing patients with active tuberculosis from asymptomatic latently infected individuals have been described but, no consensus exists for the composition of optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Overall design: We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting.

A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection [Leicester non-progressor]

Submitted by Gene Expression Omnibus on 20-APR-2018

Total RNA was isolated from 1 ml whole blood using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Applied Biosystems/Thermo Fisher Scientific) according to the manufacturer's instructions. Globin RNA was depleted from total RNA (1.5–2 µg) using the human GLOBINclear kit (Thermo Fisher Scientific) according to manufacturer's instructions. RNA yield of total and globin-reduced RNA was assessed using a NanoDrop™ 8000 spectrophotometer (Thermo Fisher Scientific). Quality and integrity of total and globin-reduced RNA were assessed with the HT RNA Assay reagent kit (Perkin Elmer) using a LabChip GX bioanalyser (Caliper Life Sciences/Perkin Elmer) and assigned an RNA Quality Score (RQS). Samples (200 ng) with an RQS > 6 were used to prepare a cDNA library using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). The tagged libraries were sized and quantitated in duplicate (Agilent TapeStation system), using D1000 ScreenTape and reagents (Agilent), normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired end reads (75 bp) per sample.

A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection [Leicester non-progressor]

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