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Sample GSM4498833 Query DataSets for GSM4498833
Status Public on Apr 28, 2020
Title lasR_coculture_WT_rep1
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) [email protected]
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 SAMN14734719
SRA SRX8180524

Supplementary file Size Download File type/resource
GSM4498833_Pa_lasR_coculture_1.csv.gz 213.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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