Library of 5-cleavage fragments with 2,3-cP_exponential growth
SAMN19090735
External Id
University Leipzig
INSDC center name
2022-01-13T00:00:00Z
INSDC first public
2023-12-07T21:08:34.844Z
INSDC last update
SRS8910555
INSDC secondary accession
live
INSDC status
Microbe, viral or environmental
NCBI submission model
Microbe.1.0
NCBI submission package
SRS8910555
SRA accession
2021-01-25
collection date
180 ml medium 63 (DSMZ) was inoculated with 400 l liquid culture of Desulfovibrio vulgaris (DSM 644) and incubated at 37C for 92 h (exponential growth) under anaerobic conditions. After total RNA isolation with TRIzolTM reagent (Thermo Scientific), 1 g total RNA was used for degradation of RNAs with 5-triphosphates or 5-monophosphates with RppH and Xrn1. After the enrichment of RNAs with 5-OH, sample a hairpin adapter was ligated to mature tRNAs with CCA-ends (Erber et al. 2019, https://doi.org/10.1080/15476286.2019.1664250) to block them for further ligation reactions (tRNA blocking). 40 pmol DNA-adapter with a unique molecular identifier that was pre-adenylated with the TS2126 RNA ligase 1 was used in ligation reaction with enriched RNA using T4 RNA ligase 2 truncated KQ. Then, ligation product was reverse transcribed by SuperScript IV and RNA was degraded using NaOH. Second adapter was ligated to gel-purified cDNA with T4 RNA ligase 1 and used for DNA amplification with TruSeq Small RNA Illumina primers. Sample was sequenced with ~ 30M reads and 150 bp paired-end.
description
Germany: Leipzig
geo loc name
Library of 3-cleavage fragments with 5-OH_exponential growth
isolation source
Nitratidesulfovibrio vulgaris str. Hildenborough
http://purl.obolibrary.org/obo/NCBITaxon_882
organism
cell culture
sample type
Hildenborough
strain
AtRNL_1
title
type strain of Desulfovibrio vulgaris
type material