Characterizing Mucispirillum transcriptome in mice

Nucleic acids were extracted from collected samples, and DNase was digested twice and checked to be DNA free using PCR. rRNA was removed using the Ribo-Zero bacterial kit (Illumina, San Diego, CA) and evaluated using an RNA HighSens kit (Experion, Hercules, CA). RNA was prepared for multiplexed Illumina RNA-seq (NEBNext Ultra RNA library prep kit for Illumina with NEBNext multiplex oligonucleotides; New England Biolabs, Ipswich, MA) and sequenced on the HiSeqV4 SR100 platform (Campus Science Support Facilities GmbH, Vienna, Austria). Sequence data are available at the European Nucleotide Archive (ENA) under BioProject no. PRJEB13534. Published metatranscriptomic data sets from mice with detectable levels of Mucispirillum were downloaded from the National Center for Biotechnology Information Short Read Archive database and quality filtered using Trimmomatic (89 (link)). Reads were mapped to the M. schaedleri genome using BWA (90 (link)) and analyzed with HTSeq (91 (link)).

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Loy A., Pfann C., Steinberger M., Hanson B., Herp S., Brugiroux S., Gomes Neto J.C., Boekschoten M.V., Schwab C., Urich T., Ramer-Tait A.E., Rattei T., Stecher B, & Berry D. (2017). Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems, 2(1), e00171-16.

Publication 2017

Ribo-Zero bacterial kit NEBNext multiplex oligonucleotides

Bacterial Collected samples Dnase European Library Mice Nucleic acids Nucleotide Oligonucleotides Rna seq Rrna

Corresponding Organization :

Other organizations : University of Vienna, Ludwig-Maximilians-Universität München, German Center for Infection Research, University of Nebraska–Lincoln, Wageningen University & Research

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Variable analysis

independent variables

Presence/absence of Mucispirillum in mice

dependent variables

Metatranscriptomic data
Gene expression levels

control variables

RNA extraction and purification procedures
Sequencing platform and parameters

controls

DNase digestion and PCR to check for DNA contamination
RRNA removal using Ribo-Zero bacterial kit
RNA quality evaluation using Experion RNA HighSens kit

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