U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from BioSample

SRX25441987: GSM8416030: PccC1; Pectobacterium carotovorum subsp. carotovorum; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 30.1M spots, 6.1G bases, 1.7Gb downloads

External Id: GSM8416030_r1
Submitted by: Microbiology, Pusan National University
Study: RNA-seq based transcriptome analysis of plant pathogens under salt stress condition
show Abstracthide Abstract
Plant pathogens require lethal virulence factors, susceptible hosts, and optimal environmental conditions for disease establishment. High soil salinity, exacerbated by climate change, significantly impacts agro-biological ecosystems. However, the overall interactions between plant pathogens and salt stress are not fully characterized or understood. This study examines the effects of salt stress on representative plant pathogens: Burkholderia gladioli, Pectobacterium carotovorum subsp. carotovorum, and Ralstonia solanacearum. Using pan-genome-based comparative transcriptomics, we analyzed the comprehensive alterations within the biological systems of plant pathogens when treated with 200 mM NaCl. Our results highlight the differential responses between salt-sensitive and salt-tolerant pathogens to salt stress. Overall design: To induce salt stress, 200 mM NaCl was applied to salt-sensitive (B. gladioli and R. solanacearum) and salt-tolerant (Pcc) pathogens. For each plant pathogen, cultures without NaCl addition were used as negative controls. After 2 hours of exposure to salt stress, we examined changes in gene expression patterns. Each sample was prepared in triplicate.
Library:
Name: GSM8416030
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: For sequencing library preparation, 4 ml of bacterial cultures were harvested by centrifugation at 5000 × g for 10 minutes and then stabilized using the RNAprotect Bacteria Reagent (Qiagen, CA, USA). Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA quality and quantity were measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (New England Biolabs, MA, USA). The enriched RNA was then used to construct cDNA libraries with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, CA, USA) according to the manufacturer's protocol. Paired-end NGS sequencing was performed on the Illumina NovaSeq 6000 platform (Macrogen, Seoul, Korea).
Runs: 1 run, 30.1M spots, 6.1G bases, 1.7Gb
Run# of Spots# of BasesSizePublished
SRR2995187630,064,2566.1G1.7Gb2024-08-08

ID:
34121454

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...