|
| Status |
Public on Feb 18, 2020 |
| Title |
EDTA_3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture (LBN media)
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
media additive(s): EDTA
|
| Growth protocol |
Bacteria were grown aerobically overnight in LB at 37oC. The next day, bacteria were diluted 100-fold into 20 ml of fresh LBN 6.5 then aliquoted into 4 tubes containing 5 ml each. Tubes were incubated anaerobically at 37oC under static conditions for 3 hr. Final concentrations of 1 mM EDTA and/or 15 mM NaNO2 were added to each tube. Then, cells were incubated for an additional 2.5 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Bacteria Protect Rneasy Mini kit, Epicentre Ribo-Zero rRNA removal kit
mRNA reverse transcribed using Illumina TruSeq stranded mRNA library preparation kit. Libraries barcoded with 8bp oligos then amplified for 15 cycles
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ribosomally depleted RNA
|
| Data processing |
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the PA14 genome using STARv2.5.2b
read count tables were generated using htseq-count v.2.5
Genome_build: PAO1 NC_002516 (GenBank gene annotations)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample
|
| |
|
| Submission date |
Dec 26, 2019 |
| Last update date |
Feb 18, 2020 |
| Contact name |
Erin Gill |
| E-mail(s) |
[email protected]
|
| Organization name |
University of British Columbia
|
| Street address |
2259 Lower Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE142611 |
AB569, A Nontoxic Chemical Tandem That Kills Major Human Pathogenic Bacteria |
|
| Relations |
| BioSample |
SAMN13682996 |
| SRA |
SRX7442758 |
