|
| Status |
Public on Aug 08, 2023 |
| Title |
39b11 Transposon mutant rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
39b11 transposon mutant bacterial cell
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: 98-37-09
transposon: A1S_3277::Tn5
treatment: 0.15 µg/mL levofloxacin for 6 hrs
|
| Treatment protocol |
A.baumannii wild type and 39b11 mutant (A1S_3277::Tn5) were treated with 0.15 µg/mL levofloxacin during 6hr growth period.
|
| Growth protocol |
A.baumannii wild type and 39b11 mutant (A1S_3277::Tn5) cells were grown for 6 hrs in 25 mL of human serum at 37 degrees celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed with TE buffer and total bacterial RNA was isolated using a Qiagen Rneasy kit according to the manufacturer's instructions. RNA was further Dnase treated and re-isolated with the Rneasy kit.
To construct sequencing libraries, cDNA synthesis was performed, the 3′ ends were adenylated and adaptors were ligated. Paired-end sequencing was performed with Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling performed using RTA3 software, sequence adapters removed and low quality reads filtered using fastQC software (v 0.11.9).
Reads were mapped to reference genome A.baumannii 17978 (ASM1542v1) by HISAT2 (v 2.2.1).
Assembled transcripts were generated and merged with StringTie (v 2.1.5).
Transcripts were quantified and gene expression levels determined using Cufflinks software (v 2.2.1).
Differential Gene Expression Analysis was conducted using DESeq software (v 3.14). A false detection rate (FDR) ≤ 0.05 and the absolute value of Log2 ratio ≥ 1 were used as the default threshold to identify significant Differentially Expressed Genes (DEGs)
DEGs were classified based on their Gene Ontology (GO) functional terms and KEGG pathway enrichment analysis using topGO software (v 3.14).
Genome_build: ASM1542v1
Supplementary_files_format_and_content: Raw counts and FPKM abundance counts in text document files. DEG analysis with KEGG GO annotations in Excel comma separated file.
|
| |
|
| Submission date |
Dec 03, 2021 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Mikaeel Imran Young |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
University of Rochester
|
| Department |
Microbiology and Immunology
|
| Lab |
Paul Dunman
|
| Street address |
601 Elmwood Ave, Rm 211311B , MRBX
|
| City |
Rochester |
| State/province |
New York |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL28641 |
| Series (1) |
| GSE190119 |
Transcriptome analysis of A.baumannii 98-37-09 wild type compared to YhaK Tn mutant under antibiotic treatment in human serum. |
|
| Relations |
| BioSample |
SAMN23591041 |
| SRA |
SRX13303188 |
