5'-specific RNA-Seq of Corynebacterium glutamicum wildtype, deletion mutant sigE and deletion mutant cseE reveals TSS and promoters depending on SigE and thereby overlapping SigH and SigE sigma factor regulons.
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ABSTRACT: Total RNA was isolated from 3 biological replicates of C. glutamicum wildtype, deletion mutant sigE and deletion mutant cseE cells by a Quick-RNA Miniprep Plus kit (Zymo Research). The samples were treated with DNase (Roche Diagnostics) and RNA was purified with an RNA Clean&Concentrator-5 kit (Zymo Research). A primary 5′-end-specific cDNA library was constructed for sequencing with the aim of defining TSSs using the protocol described previously (Albersmeier et al., 2017; Wittchen et al., 2018). Briefly, rRNA was depleted and the RNA samples were treated with a terminator 5'-phosphate-dependent exonuclease (Illumina) to remove non-primary transcripts. The primary 5'-triphosphate ends of the primary transcripts were treated with RNA 5'-polyphosphatase to convert them into 5'-mono phosphate ends, and the 5'-adapter was ligated to the produced 5'-ends. Then, reverse transcription with a stem-loop DNA adapter was carried out and the library was amplified. The primary 5'-end cDNA library was then purified and size-selected for fragments approximately 100-1000 nt in size by gel electrophoresis and quantified. The fragments were finally sequenced with an Illumina MiSeq.
INSTRUMENT(S): Illumina MiSeq
ORGANISM(S): Corynebacterium glutamicum
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PROVIDER: E-MTAB-12458 | biostudies-arrayexpress |
SECONDARY ACCESSION(S): E-MTAB-12457
REPOSITORIES: biostudies-arrayexpress
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