|
Status |
Public on May 18, 2022 |
Title |
2_supernatant_rep1 |
Sample type |
SRA |
|
|
Source name |
bacterial cells
|
Organism |
Pseudomonas aeruginosa |
Characteristics |
strain: PA14 time point: 120 min treatment: S. aureus supernatant
|
Treatment protocol |
Either 25% (v/v) of media 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
|
|
|
Submission date |
Oct 15, 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 |
GPL28386 |
Series (1) |
GSE185963 |
Pseudomonas aeruginosa gene regulation by Staphylococcus aureus exoproducts |
|
Relations |
BioSample |
SAMN22321193 |
SRA |
SRX12629984 |