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| Status |
Public on Aug 08, 2024 |
| Title |
PccT1 |
| Sample type |
SRA |
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| Source name |
PCC21
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| Organism |
Pectobacterium carotovorum subsp. carotovorum |
| Characteristics |
strain: PCC21
treatment: 200 mM NaCl
genotype: wild type
time: 2 hours
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| Growth protocol |
Burkholderia gladioli BSR3 and Pectobacterium carotovorum subsp. carotovorum PCC21 were cultured in LB broth at 28°C. Ralstonia solanacearum GMI1000 were cultured at 28°C in casamino acid peptone glucose (CPG) medium (1 g/L casamino acids, 10 g/L peptone, 5 g/L glucose). All liquid cultures were incubated in a shaker-incubator at 200 rpm. Bacterial cultures in the early exponential phase were prepared for both salt-susceptible and salt-tolerant pathogens. To induce a salt stress response, these cultures were exposed to 200 mM NaCl for 2 hours. Cultures without NaCl addition were used as negative controls.
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| Extracted molecule |
total RNA |
| Extraction 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Pcc treated with 200 mM NaCl
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| Data processing |
Raw FASTQ reads were refined by eliminating sequences with suboptimal quality scores, using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). A in-house Python script ensured the alignment of the forward and reverse reads.
Filtered clean reads were mapped to reference genome of each bacteria using the Burrows-Wheeler Aligner (BWA), employing the maximal exact match approach.
Generated SAM files were subsequently sorted by genomic coordinates using the SAMtools program.
The Subread package and featureCounts tool tallied the reads for each coding sequence.
Gene transcript levels were assessed using the RPKM metric.
Assembly: Burkholderia gladioli BSR3 GCF_000194745.1
Assembly: Pectobacterium carotovorum subsp. carotovorum PCC21 GCF_000294535.1
Assembly: Ralstonia solanacearum GMI1000 GCF_000009125.1
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample
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| Submission date |
Jul 24, 2024 |
| Last update date |
Aug 08, 2024 |
| Contact name |
Jungwook Park |
| E-mail(s) |
[email protected]
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| Organization name |
Pusan National University
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| Department |
Microbiology
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| Street address |
Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea
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| City |
Busan |
| ZIP/Postal code |
ASI|KR|KS012|PUSAN |
| Country |
South Korea |
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| Platform ID |
GPL34741 |
| Series (1) |
| GSE272984 |
RNA-seq based transcriptome analysis of plant pathogens under salt stress condition |
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| Relations |
| BioSample |
SAMN42783714 |
| SRA |
SRX25441990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8416033_PccT1_RPKM.txt.gz |
907.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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