|
| Status |
Public on Sep 14, 2023 |
| Title |
AB5075_3 |
| Sample type |
SRA |
| |
|
| Source name |
Acinetobacter baumannii AB5075
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: Acinetobacter baumannii AB5075
|
| Growth protocol |
Overnight cultures of A. baumannii AB5075 and CRL 2244 with OD adjusted to 600 nm at 4.0 were centrifuged and resuspended in 3 mL of BHI broth and incubated for 90 min at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Direct-zol RNA Kit (Zymo Research)
Illumina RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Low-quality reads were removed using Trimmomatic v0.39
Reads were aligned witth Burrows Wheeler Alignment software (BWA) v0.7.17
Bigwig files were generated with custom bash scripts and BEDtools
Read counts per gene were determined using featureCounts v1.6.4
RNA-seq differential expression analysis was performed using DESeq2
Supplementary files format and content: .txt files containing the output of featureCounts for each sample
|
| |
|
| Submission date |
Jul 07, 2023 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Sieira Rodrigo |
| E-mail(s) |
rsieira@leloir.org.ar
|
| Organization name |
Fundacion Instituto Leloir
|
| Street address |
Av. Patricias Argentinas 435
|
| City |
Buenos Aires |
| ZIP/Postal code |
C1405 BWE |
| Country |
Argentina |
| |
|
| Platform ID |
GPL28641 |
| Series (1) |
| GSE236782 |
Phenotypic and transcriptional analysis of the antimicrobial effect of lactic acid bacteria on carbapenem-resistant Acinetobacter baumannii: Lacticaseibacillus rhamnosus CRL 2244 an alternative strategy to fight it |
|
| Relations |
| BioSample |
SAMN36356468 |
| SRA |
SRX20933204 |
