|
| Status |
Public on May 31, 2019 |
| Title |
LB3_1 |
| Sample type |
SRA |
| |
|
| Source name |
A118_LB
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: A118
condition: LB
biological replicate: 3
|
| Treatment protocol |
Bacteria were cultured in Luria Bertani broth (LB) with or without PF for 18 h.
|
| Growth protocol |
Bacteria were grown in a rotary shaker with agitation at 37oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRI REAGENT® Kit
Illumina RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A118_4
|
| Data processing |
Low-quality reads were removed using Trimmomatic v0.32
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
Bigwig files were generated with custom bash scripts and BEDtools
RNA-seq differential expression analysis was performed using DESeq
Genome_build: assembly of Acintetobacter baumannii A118 (that was performed in RAST)
Supplementary_files_format_and_content: raw counts and tsv file generated by DESeq provides gene ID, base mean reads, fold-change, log2 fold-change, p-value and adjusted p-value for the expression of each gene.
|
| |
|
| Submission date |
May 30, 2019 |
| Last update date |
May 31, 2019 |
| Contact name |
M. S. Ramirez |
| Organization name |
California State University Fullerton
|
| Street address |
800 N. State College Blvd
|
| City |
Fullerton |
| State/province |
CA |
| ZIP/Postal code |
DBH-117A |
| Country |
USA |
| |
|
| Platform ID |
GPL24655 |
| Series (1) |
| GSE131949 |
Human pleural fluid elicits pyruvate and phenylalanine metabolism in Acinetobacter baumannii to enhance cytotoxicity and immune evasion |
|
| Relations |
| BioSample |
SAMN11891349 |
| SRA |
SRX5931295 |
