Metatranscriptome Sequencing and Analysis

Metatranscriptomes from Station 2 were obtained as described in Kitzinger et al.^{31 (link)}. To enrich for mRNA, ribosomal RNA (rRNA) was depleted from total RNA using the Ribo-Zero™ rRNA Removal Kit for bacteria (Epicentre). mRNA-enriched RNA was converted to cDNA and prepared for sequencing using the ScriptSeq™ v2 RNA-Seq Library preparation kit (Epicentre) and sequenced on an Illumina MiSeq using a 600 cycle kit. Metatranscriptomes were separated into ribosomal and non-ribosomal partitions using SortMeRNA v. 2.1 (ref. ^{82 (link)}). Metatranscriptome sequencing statistics are listed in Supplementary Table 6.

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Kitzinger K., Marchant H.K., Bristow L.A., Herbold C.W., Padilla C.C., Kidane A.T., Littmann S., Daims H., Pjevac P., Stewart F.J., Wagner M, & Kuypers M.M. (2020). Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean. Nature Communications, 11, 767.

Publication 2020

Ribo-Zero™ rRNA Removal Kit for bacteria ScriptSeq™ v2 RNA-Seq Library preparation kit

Bacteria Cdna Library Mrna Ribosomal Ribosomal rna Rna seq

Corresponding Organization : Max Planck Institute for Marine Microbiology

Other organizations : University of Vienna, Georgia Institute of Technology

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Variable analysis

independent variables

Method of rRNA depletion using Ribo-Zero™ rRNA Removal Kit for bacteria (Epicentre)
RNA-Seq library preparation using the ScriptSeq™ v2 RNA-Seq Library preparation kit (Epicentre)
Sequencing platform used: Illumina MiSeq with a 600 cycle kit

dependent variables

Metatranscriptome sequencing data

control variables

RNA samples from Station 2 as described in Kitzinger et al. (2018)
Separation of metatranscriptomes into ribosomal and non-ribosomal partitions using SortMeRNA v. 2.1

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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