|
| Status |
Public on Mar 18, 2022 |
| Title |
E104 rhlR- rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
growth phase: OD600=2.0
growth medium: LB+MOPS liquid culture
genotype/variation: rhlR-deletion
|
| Treatment protocol |
10 uM C4-HSL and 2 uM 3oxoC12-HSL synthetic signals were added to WT samples (samples E104sig1-3)
|
| Growth protocol |
All cells were grown in 25 ml LB+MOPS broth in a 250 ml baffled flask incubated at 37C with 250 rpm shaking from a starting OD600 of 0.001.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was preserved immediately upon cell harvest using Qiagen RNAprotect. Cells were lysed using a bead-beating protocol and mRNA was extracted using Qiagen RNEasy miniprep columns, followed by DNAse I treatment and cleanup using another round of RNEasy-based purification. rRNA was removed using Illumina RiboZero protocol.
150bp PE Illumina TruSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
E104rhlR3
|
| Data processing |
Illumina bcl2fastq2 Conversion Software v2.18 for fastq file generation
Quality filtering and adapter removal using Trim Galore!
Alignment to reference using subread-align
Count matrix generation using featureCounts
Assembly: E104 complete genome: PRJNA784987, SAMN26565086, JGI-IMG#2913679597
Supplementary files format and content: Raw count data in a tab-delimited text file with genes as rows and samples as columns
|
| |
|
| Submission date |
Mar 13, 2022 |
| Last update date |
Mar 18, 2022 |
| Contact name |
Kyle Lowe Asfahl |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Street address |
1705 NE Pacific St
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL24583 |
| Series (1) |
| GSE198534 |
Genetic and transcriptomic characteristics of RhlR-dependent quorum sensing in cystic fibrosis isolates of Pseudomonas aeruginosa: isolate E104 |
|
| Relations |
| BioSample |
SAMN26645028 |
| SRA |
SRX14454193 |
