|
| Status |
Public on Oct 12, 2022 |
| Title |
WCS365WT_media_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
plant growth promoting Pseudomonas bacteria
|
| Organism |
Pseudomonas fluorescens |
| Characteristics |
background strain: WCS365
genotype: wild-type
treatment: grown in M9 minimal media
|
| Treatment protocol |
BMDMs were either left unstimulated, or stimulated with LPS (100 ng/mL) for 6 hrs.
|
| Growth protocol |
1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions and stored in RNAprotect Bacteria Reagent (Qiagen) if extraction was not perfomed immediately.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...
|
| |
|
| Submission date |
Dec 08, 2021 |
| Last update date |
Oct 12, 2022 |
| Contact name |
Chrisitna L Wiesmann |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of British Columbia
|
| Department |
Microbiology and Immunology
|
| Lab |
Haney
|
| Street address |
1365 - 2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL31044 |
| Series (1) |
| GSE190448 |
The ColR/S two-component system is a conserved determinant of host association across Pseudomonas species |
|
| Relations |
| BioSample |
SAMN23787794 |
| SRA |
SRX13351713 |
