|
| Status |
Public on May 18, 2022 |
| Title |
20_supernatant_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Pseudomonas aeruginosa PA14 |
| Characteristics |
strain: PA14
time point: 20 min
treatment: S. aureus supernatant
|
| Treatment protocol |
25% (v/v) of media, media with the indicated products, or S. aureus supernatant was added to the sample.
|
| Growth protocol |
P. aeruginosa was grown in a modified M63 medium shaking at 300 rpm at 37C to OD600 = 0.5 before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA Purification Plus Kit (Norgen)
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reads were cut with Cutadapt. Sequence AGATCGGAAGAGC was removed.
Reads were trimmed with Trimmomatic for single end using leading (3), trailing (3), sliding window (4-15), and minimum length of 10.
Rockhopper was run to match reads to P. aeruginosa UCBPP-PA14 genome and compare expression levels.
Genome_build: RefSeq NC_008463.1
Supplementary_files_format_and_content: txt files were generated using Rockhopper
Supplementary_files_format_and_content: Raw Counts Normalized Counts RPKM Expression
|
| |
|
| Submission date |
Oct 19, 2021 |
| Last update date |
May 18, 2022 |
| Contact name |
Anupama Khare |
| E-mail(s) |
anupama.khare@nih.gov
|
| Organization name |
National Cancer Institute
|
| Street address |
37 Convent Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL30881 |
| Series (1) |
| GSE186138 |
Pseudomonas aeruginosa gene regulation by Staphylococcus aureus supernatant or added secreted products |
|
| Relations |
| BioSample |
SAMN22406788 |
| SRA |
SRX12686260 |
