Library of 3-cleavage fragments with 5-OH_exponential growth
SAMN19090734
External Id
University Leipzig
INSDC center name
2022-01-13T00:00:00Z
INSDC first public
2023-12-07T21:08:34.810Z
INSDC last update
SRS8910554
INSDC secondary accession
live
INSDC status
Microbe, viral or environmental
NCBI submission model
Microbe.1.0
NCBI submission package
SRS8910554
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 short RNA enrichment with polyethylene glycol and NaCl (Lu et al. 2007, https://doi.org/10.1016/j.ymeth.2007.05.002). After the enrichment, 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 Arabidopsis thaliana tRNA ligase variant AA (K152A,D726A). Resulting 2-phosphate at the ligation site was removed by Tpt1 phosphotransferase. 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 5-cleavage fragments with 2,3-cP_exponential growth
isolation source
Nitratidesulfovibrio vulgaris str. Hildenborough
http://purl.obolibrary.org/obo/NCBITaxon_882
organism
cell culture
sample type
Hildenborough
strain
T4RNL_1
title
type strain of Desulfovibrio vulgaris
type material