Computational protocol: In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways

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Protocol publication

[…] cDNA libraries were constructed following a standard protocol (, ). Briefly, RNA was polyadenylated at 3′ end and ligated to an adaptor at 5′ end after treatment with tobacco acid pyrophosphatase. First-strand cDNA was synthesized using oligo(dT)-adaptor and M-MLV reverse transcriptase. The linear amplified cDNAs were multi-plexed and sequenced using Illumina HiSeq. Reads were mapped to Salmonella genome using READemption; 5′ end coverage was visualized in IGB. The RNase E sites, which are depleted 5′ ends in the rneTS samples relative to WT at 44°C, were identified using DESeq2. […]

Pipeline specifications

Software tools READemption, DESeq2
Application RNA-seq analysis
Chemicals Nucleotides, Uridine