Fecal Escherichia coli ribosomal RNA-depleted RNA sequencing after reconstitution with monoclonal secretory IgA B8-030
Prior to cDNA library generation, probe-based depletion of ribosomal RNA was performed on 2 ?g of total RNA using a Ribominus Transcriptome Isolation Kit for Yeast and Bacteria (Thermo fisher Scientific, Invitrogen) according to the producer's protocol. Thereafter, the remaining RNA was concentrated using an RNA Clean & Concentrator-5 kit (Zymo Research) and used to make cDNA libraries using an Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina) in combination with IDT for Illumina  TruSeq RNA UD Indexes (Illumina). The Illumina protocol was followed exactly from the point of RNA fragmentation which means omission of the initial polyA selection steps.