Transcriptomics

Dataset Information

4

Comparative analysis of bacterial transcriptome using DNA microarray and next generation sequencing technologies


ABSTRACT: Validation of Lactobacillus plantarum WCFS1 transcriptome profile using RNA sequencing (direct cDNA sequencing and 3'-UTR sequencing) in comparison with DNA microarray as a reference platform. Transcriptome analysis was performed on total RNA and enriched mRNA of L. plantarum WCFS1 grown in CDM or MRS media. Samples were hybridized in a loop design, hybridizing each sample twice, once for each dye This Series represents the DNA microarray experiments only.

ORGANISM(S): Lactobacillus plantarum  

SUBMITTER: Milkha M Leimena   Eddy J Smid  Michiel Kleerebezem  Roger S Bongers  Michiel Wels 

PROVIDER: E-GEOD-35754 | ArrayExpress | 2012-07-09

SECONDARY ACCESSION(S): GSE35754PRJNA152097

REPOSITORIES: GEO, ArrayExpress

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Publications

Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies.

Leimena Milkha M MM   Wels Michiel M   Bongers Roger S RS   Smid Eddy J EJ   Zoetendal Erwin G EG   Kleerebezem Michiel M  

Applied and environmental microbiology 20120406 12


RNA sequencing is starting to compete with the use of DNA microarrays for transcription analysis in eukaryotes as well as in prokaryotes. The application of RNA sequencing in prokaryotes requires additional steps in the RNA preparation procedure to increase the relative abundance of mRNA and cannot employ the poly(T)-primed approach in cDNA synthesis. In this study, we aimed to validate the use of RNA sequencing (direct cDNA sequencing and 3'-untranslated region [UTR] sequencing) using Lactobaci  ...[more]

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