 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 28, 2020 |
| Title |
lasR_monoculture_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
colony biofilm
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PA14
taxonomy id: 652611
|
| Treatment protocol |
P. aerguinosa PA14 ∆lasR was grown above either ∆lasR or WT.
|
| Growth protocol |
P. aeruginosa strains used for initial inoculum were grown for 16 h overnight in 5 mL LB on roller drum at 37 ℃. A 200 µL aliquot of optical density normalized (OD 600 = 1) cultures of PA14 or PA14 ∆lasR were evenly spread on an LB plate with sterile glass beads and briefly allowed to dry. Two isopore 0.2 µm PC membrane filters were stacked on the lawn (37 mm diameter filter directly on lawn then 25 mm diameter filter on top), and 15 µL of normalized (OD 600 = 1) ∆lasR cultures were spotted on the top-most filter. After 16 h incubation at 37 ℃, the top filter was collected and ∆lasR cells were resuspended in 1 mL LB by 5 min of vigorous shaking using a Genie Disruptor (Zymo) for collection of cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to manufacturer’s protocol with the QIAGEN RNeasy Mini kit
RNA was treated with Invitrogen Turbo DNA-Free kit and ribo-depletion performed using RiboZero (bacteria). Library prep was done as the Illumina TrueSeq Stranded RNAseq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls - Illumina native app
Trimming - Illumina native app to trim adapter sequences
Quality Control CLC Genomics Workbench: quality score = 0.05, ambiguous bases = 2, auto adapter trim = NO, trim bases 5' and 3', filter length above = NO, filter length below = NO
Alingment to Pseudomonas aeruginosa strain PA14 genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
Reporting - CLC Workbench export raw counts, TPM, CPM and RPKM
Genome_build: UCBPP-PA14
Supplementary_files_format_and_content: csv including TPM
|
| |
|
| Submission date |
Apr 27, 2020 |
| Last update date |
Apr 29, 2020 |
| Contact name |
Mark Adams |
| E-mail(s) |
Mark.Adams@jax.org
|
| Organization name |
The Jackson Laboratory
|
| Street address |
10 Discovery Drive
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21297 |
| Series (1) |
| GSE149385 |
Transcriptional profiling of Pseudomonas aeruginosa ∆lasR in mono- and co-culture with wild type. |
|
| Relations |
| BioSample |
SAMN14734720 |
| SRA |
SRX8180523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4498832_PA_lasR_monoculture_3.csv.gz |
212.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
