|
| Status |
Public on Sep 01, 2023 |
| Title |
Ptab5_2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf intercellular wash fluid
|
| Organism |
Pseudomonas amygdali pv. tabaci |
| Characteristics |
strain: 11528
tissue/sample type: leaf intercellular wash fluid
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen samples were homogenized in 2mL homogenization tubes with high-density zirconium beads (Glen Mills) using a Geno/Grinder (SPEX SamplePrep) for 1 min at 1,750 Hz with a LN2 chilled sample holder. RNA was extracted using the DirectZol RNA miniprep kit (Zymo Research). RNA samples were DNAse treated with the Turbo DNAse (Thermo-Fisher) followed by cleanup with the Monarch RNA Cleanup Kit (NEB). Reagents were used according to the manufacturer’s recommendations.
Plant mRNA sequencing libraries were prepared with the Illumina-compatible KAPA Stranded mRNA-seq Kit (Roche) by the Georgia Genomics and Bioinformatics Core (GGBC). The Psy RNA samples were rRNA depleted using the RiboMinus Bacterial kit (Thermo Fisher) and libraries were prepared with the Illumina-compatible KAPA Stranded RNA-seq Kit (Roche) by the GGBC. The Pta RNA samples were rRNA depleted using both RiboZero Plant and RiboZero Bacteria (Illumina) in combination and RNA sequencing libraries were prepared in-house using the TruSeq Stranded Total RNA kit (Illumina). Library prep kits were used according to the manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
featureCounts_mapped_results_Ptab_4DE.txt
|
| Data processing |
Alignment: HISAT2 v2.2.1 (plant) or bowtie2 v (bacterial)
Quantification: StringTie v2.2.0 (plant) or featureCounts (bacterial)
Expression Analysis: DESeq2
Assembly: N. benthamiana Genome v1.0.1 with NbD transcriptome, P. syringae B728a (Genbank: CP000075.1), and P. amygdali pv. tabaci (Genbank: NZ_CP042804.1 and NZ_CP042805.1).
Supplementary files format and content: Output from StringTie (plant) or featureCounts (bacterial)
|
| |
|
| Submission date |
Apr 23, 2022 |
| Last update date |
Sep 01, 2023 |
| Contact name |
David Baltrus |
| E-mail(s) |
baltrus@email.arizona.edu
|
| Organization name |
University of Arizona
|
| Street address |
1140 E. South Campus Drive
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85721-0036 |
| Country |
USA |
| |
|
| Platform ID |
GPL32197 |
| Series (1) |
| GSE201377 |
Dual-transcriptomic analysis of Nicotiana benthamiana and two compatible Pseudomonas strains |
|
| Relations |
| BioSample |
SAMN27749449 |
| SRA |
SRX14979888 |
