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Sample GSM5176182 Query DataSets for GSM5176182
Status Public on Sep 13, 2022
Title dksA Cu3
Sample type SRA
 
Source name Batch culture Mueller Hinton broth
Organism Acinetobacter baumannii
Characteristics strain: ATCC 17978
genotype: dksA::kan
growth phase: Exponential
treatment: CuSO4
Extracted molecule total RNA
Extraction protocol Bacterial cells were collected, flash frozen on dry ice ethanol bath, and RNA was harvested using Trizol (Ambion) reagent. For isolation and purification of total RNA from cells, RNeasy Qiagen was used.
Libraries were constructed using Universal Prokaryotic RNA-Seq Library preparation kit (Tecan, USA) according to the manufacturer protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalling was done using bcl2fastq2 V2.20 (Illumina, USA).
QC was performed using fastQC (v0.11.9)
Reads were trimmed using bbduk (v38.79) using the adapters.fa file provided with bbduk and parameters ktrim=r k=23 mink=11 hdist=1 qtrim2=t trimq=10 tpe tbo
Reads were mapped using bbmap (v38.79) with parameters k=13 and ambig=toss against the Acinetobacter baumannii genome (accession CP000522) and plasmids (accessions CP000523, CP012004, CP012005)
Reads were sorted using samtools (v1.6)
Reads over CDS features were quantified using HTSeq (v0.12.4)
Genome_build: CP000522.1, CP000523.1, CP012004.1, CP012005.1
Supplementary_files_format_and_content: Tab separated values containing read counts per feature in each condition
 
Submission date Mar 17, 2021
Last update date Sep 13, 2022
Contact name Lars Barquist
E-mail(s) lars.barquist@helmholtz-hiri.de
Organization name Helmholtz Institute for RNA-based Infection Research
Street address Josef-Schneider-Straße 2 / Bau D15
City Würzburg
State/province Bayern
ZIP/Postal code 97080
Country Germany
 
Platform ID GPL28641
Series (1)
GSE169081 DksA acts as a transcriptional switch in stress and virulence in Acinetobacter baumannii
Relations
BioSample SAMN18332790
SRA SRX10366528

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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