|
| Status |
Public on Dec 15, 2022 |
| Title |
Cbl_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial planktonic cells grown in Müller Hinton broth
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: ABUW_1016-125:T26
genotype: Tn mutant
|
| Growth protocol |
Three independent A. baumannii parental AB5075_UW and AB02746 (ABUW_1016-125:T26) mutant cultures were grown overnight in 5ml Müller Hinton broth at 37°C, with shaking. The overnight cultures were diluted 1:100 in MH and grown to mid-exponential phase cultures (15 mL, OD600 ~ 0.6) at 37°C, with shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy mini kit (Qiagen) and DNA digestion was performed on the total RNA using DNaseI (TURBO DNA-freeTM kit, Invitrogen).
Ribosomal RNA was depleted using Ribozero magnetic kit (Bacteria) (Illumina, Inc., USA) and the cDNA library was generated using TruSeq® stranded RNA preparation kit (Illumina, Inc., USA). The samples were then sequenced on Illumina NextSeq_500 (2x75bp high output flowcell) platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalling and adaptor sequence trimming were processed by commercial sequencing provider.
The sequence reads from the 6 RNA-Seq samples were aligned to the A. baumannii AB5075_UW reference genome and counted using EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes).
Differential gene expression between the parental and mutant samples were analysed using the DEseq2 R package.
|
| |
|
| Submission date |
Sep 03, 2021 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Ian Paulsen |
| E-mail(s) |
[email protected]
|
| Organization name |
Macquarie University
|
| Department |
Molecular Sciences
|
| Lab |
Paulsen Lab
|
| Street address |
14 Eastern Road
|
| City |
North Ryde |
| State/province |
New South Wales |
| ZIP/Postal code |
2109 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23966 |
| Series (1) |
| GSE183337 |
Identification of a novel LysR family transcriptional regulator controlling acquisition of sulfur sources in Acinetobacter baumannii. |
|
| Relations |
| BioSample |
SAMN21212522 |
| SRA |
SRX12007354 |
