Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens

T. L. Masters, C. A. Hilker, P. R. Jeraldo, A. V. Bhagwate, K. E. Greenwood-Quaintance, B. W. Eckloff, Nicholas D Chia, A. D. Hanssen, Matthew Abdel, J. Z. Yao, Jin Jen, Robin Patel

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

With the emergence of RNA sequencing technologies, metatranscriptomic studies are rapidly gaining attention as they simultaneously provide insight into gene expression profiles and therefore disease association pathways of microbial pathogens and their hosts. This approach, therefore, holds promise for applicability in infectious disease diagnostics. A challenge of this approach in the clinical setting is the low amount and quality of RNA, especially microbial RNA in most clinically-infected specimens. Here, we compared two commercially available stranded cDNA library preparation kits, the NuGEN Ovation SoLo RNA-Seq System and the Illumina TruSeq Stranded Total RNA, using RNA extracted from synovial and sonicate fluids from a subject with periprosthetic joint infection. The Ovation SoLo RNA-Seq System provided more useful transcriptomic data for the infecting bacterium, whereas the TruSeq Stranded Total RNA kit provided more useful human transcriptomic data.

Original languageEnglish (US)
Pages (from-to)55-62
Number of pages8
JournalJournal of Microbiological Methods
Volume154
DOIs
StatePublished - Nov 1 2018

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Gene Library
RNA
RNA Sequence Analysis
Synovial Fluid
Transcriptome
Communicable Diseases
Joints
Technology
Bacteria
Infection

Keywords

  • cDNA library preparation
  • Gene expression
  • Periprosthetic joint infection
  • RNA sequencing

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)

Cite this

Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens. / Masters, T. L.; Hilker, C. A.; Jeraldo, P. R.; Bhagwate, A. V.; Greenwood-Quaintance, K. E.; Eckloff, B. W.; Chia, Nicholas D; Hanssen, A. D.; Abdel, Matthew; Yao, J. Z.; Jen, Jin; Patel, Robin.

In: Journal of Microbiological Methods, Vol. 154, 01.11.2018, p. 55-62.

Research output: Contribution to journalArticle

Masters, TL, Hilker, CA, Jeraldo, PR, Bhagwate, AV, Greenwood-Quaintance, KE, Eckloff, BW, Chia, ND, Hanssen, AD, Abdel, M, Yao, JZ, Jen, J & Patel, R 2018, 'Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens', Journal of Microbiological Methods, vol. 154, pp. 55-62. https://doi.org/10.1016/j.mimet.2018.10.008
Masters, T. L. ; Hilker, C. A. ; Jeraldo, P. R. ; Bhagwate, A. V. ; Greenwood-Quaintance, K. E. ; Eckloff, B. W. ; Chia, Nicholas D ; Hanssen, A. D. ; Abdel, Matthew ; Yao, J. Z. ; Jen, Jin ; Patel, Robin. / Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens. In: Journal of Microbiological Methods. 2018 ; Vol. 154. pp. 55-62.
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