|
| 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 |
