|
| Status |
Public on Oct 03, 2024 |
| Title |
WT_pH6.5modifiedKB_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Pseudomonas syringae pv. tomato str. DC3000 |
| Characteristics |
cell type: bacteria
genotype: WT
treatment: pH6.5 modified KB
|
| Treatment protocol |
Wild type and ΔalgU mutant of Pst DC3000 strains were grown overnight in standard KB and then resuspended in 5 ml of pH-altered KB media at OD600 value of 0.4. These cultures were incubated for three hours at 28°C with shaking and subsequently collected for RNA extraction
|
| Growth protocol |
Pst DC3000 strainswere grown at 28°C in King’s B (KB) medium and on KB medium solidified with 1.5% (w/v) agar.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a Nanodrop and integrity assessed on a Fragment Analyzer.
Directional RNA-seq libraries were prepared from 500ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial rRNA depletion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
4030D_rawCounts:PS1-M-r1
|
| Data processing |
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Assembly: GCF_000007805.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Sep 19, 2024 |
| Last update date |
Oct 03, 2024 |
| Contact name |
Bryan Swingle |
| E-mail(s) |
[email protected]
|
| Phone |
(607) 255-7894
|
| Organization name |
USDA-ARS
|
| Lab |
Swingle Lab
|
| Street address |
302 Plant Science Building
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL34917 |
| Series (1) |
| GSE277531 |
Environmental alkalization suppresses deployment of virulence strategies in Pseudomonas syringae pv. tomato DC3000 |
|
| Relations |
| BioSample |
SAMN43821211 |
| SRA |
SRX26122088 |
