Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA266572

PRJNA266572: Identification of a Molecular Signature for Acute Lyme Disease by Human Transcriptome Profiling

Source: NCBI / GSE63085
Submission Date: Nov 07 2014
Release Date: Feb 15 2016
Update Date: May 15 2019

Summary: Lyme disease is challenging to diagnose, as clinical manifestations are variable and current tools to detect nucleic acid or antibody responses from Borrelia burgdorferi infection have low sensitivity. Here we conducted the first study of the global transcriptome of patients with Lyme disease to identify potential diagnostic biomarkers. Twenty-nine patients were enrolled and compared to 13 healthy controls at three time points after infection. Fifteen publicly available transcriptome datasets from patients in vivo or infection models in vitro were used to assess specificity of differentially expressed genes (DEGs). We found that Lyme disease results in profound and sustained changes in the patient transcriptomes, with a specific signature that shares ≤44% DEGs with other infections.

Overall Design: Gene expression profile from peripheral mononuclear blood cells (PBMC) of Lyme disease patients against healthy controls was undertaken. A total of 29 Lyme disease patients were sampled at 3 time points: acute Lyme pre-treatment (V1), 3 weeks later, immediately following completion of a standard course of antibiotics (V2), and 6 months following treatment completion (V5). 13 healthy controls were also sampled at one time point. Total RNA was extracted from 10e7 PBMC, followed by mRNA purification, paired-end barcode library preparation and sequencing on an Illumina Hiseq 2000.

GEN Datasets:
GEND000174
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: Acute Lyme pre-treatment (V1); 3 weeks later, immediately following completion of a standard course of antibiotics (V2); 6 months following treatment completion (V5); Control
Extract Protocol: PBMCs were isolated from fresh whole blood using Ficoll (Ficoll-Paque Plus, GE Healthcre) and total RNA was extracted from 10e7 PBMCs using TRIzol reagent (Life Technologies). Messenger RNA was isolated with Oligotex mRNA mini kit (Qiagen)
Library Construction Protocol: Scriptseq RNA-seq library preparation kit (Epicentre) was used to generate the RNA-seq libraries according to the manufacturer^s protocol.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Reverse
Platform: ILLUMINA
Instrument Model: Illumina Hiseq 2000
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.
mBio . 2016-02-12 [PMID: 26873097]