|
| Status |
Public on Aug 09, 2023 |
| Title |
PA14 delta-amrZ delta-ptsP cells, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
tissue: whole cells
genotype: delta-amrZ delta-ptsP
|
| Growth protocol |
P. aeruginosa strains as noted were grown for 3 d on M6301-1% agar at 25C in a standard microbiological incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NEB Monarch total RNA extraction kit according to the manufacturer's protocol for gram-negative bacteria. Ribosomal RNA was removed using the Ribo-Zero kit.
Libraries were constructed using the NEB directional kit according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MTC_3C_1
|
| Data processing |
Sequence reads were processed and trimmed using FastQC and Cutadapt
Sequence reads were aligned to genome using Bowtie 2.
Differential gene expression analysis was processed using EdgeR.
All software was set using default parameters.
Assembly: NC_008463
Supplementary files format and content: Excel file includes gene list with max group means, log2 and raw fold changes, P values and false discovery rate (FDR) P-values
|
| |
|
| Submission date |
Aug 03, 2023 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Matthew Cabeen |
| E-mail(s) |
matthew.cabeen@okstate.edu
|
| Phone |
4057446652
|
| Organization name |
Oklahoma State University
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
307 Life Science East
|
| City |
Stillwater |
| State/province |
Oklahoma |
| ZIP/Postal code |
74078 |
| Country |
USA |
| |
|
| Platform ID |
GPL26913 |
| Series (1) |
| GSE239971 |
Effect of markerless deletion of ptsP from P. aeruginosa PA14 biofilm colonies on M6301-glycerol agar for 3 d at 25C |
|
| Relations |
| BioSample |
SAMN36830808 |
| SRA |
SRX21242819 |
