|
| Status |
Public on Apr 07, 2024 |
| Title |
Pss9644, experimental, HMM, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
9644
|
| Organism |
Pseudomonas syringae pv. syringae |
| Characteristics |
strain: 9644
genotype: WT
treatment: hrp inducing minimum media (HMM)
time: 5h post inoculation
|
| Treatment protocol |
King 's B media and Hrp inducing miminum media growth protocols performed according to Moreno-Lopez et al. 2021 (https://doi.org/10.3390/microorganisms9071447)
|
| Growth protocol |
King 's B media and Hrp inducing miminum media growth protocols performed according to Moreno-Lopez et al. 2021 (https://doi.org/10.3390/microorganisms9071447)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction protocol performed according to Moreno-Lopez et al. 2021 (https://doi.org/10.3390/microorganisms9071447)
RNA was converted atNovogeneinto sequencing-ready libraries for Illumina sequencing using Illumina Ribo-Zero Plus rRNA Depletion Kit andNovogeneNGS Stranded RNA Library Prep Set (PT044)*. cDNA libraries were subjected to RNASeq, using an Illumina Novaseq 6000 system with 150-bp pair-end reads.
Prokaryotic directional mRNA preparation (rRNA removal)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ribosomal depletion
RNA_1
|
| Data processing |
The quality of the raw sequencing data was checked with FastQC version 0.11.9
Read adapters were trimmed using fastq-mcf version 1.04.807
Transcripts were aligned and counted and normalised using Salmon version 1.9.0
Assembly: GCF_023277945.1
Supplementary files format and content: Matrix table with raw transcript counts for every transcript and every sample
Supplementary files format and content: Matrix table with normalized transcript counts for every transcript and every sample
|
| |
|
| Submission date |
Feb 05, 2024 |
| Last update date |
Apr 07, 2024 |
| Contact name |
Andrea Vadillo Dieguez |
| E-mail(s) |
axv352@student.bham.ac.uk
|
| Phone |
07851339299
|
| Organization name |
University of Birmingham
|
| Street address |
Edgbaston
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL34164 |
| Series (1) |
| GSE255102 |
Transcriptome profiling of Pseudomonas syringae pv. syringae 9644 in rich media and hrp-inducing minimum media |
|
| Relations |
| BioSample |
SAMN39832743 |
| SRA |
SRX23536692 |
