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| Status |
Public on Oct 06, 2020 |
| Title |
Transcriptome analysis of Arabidopsis thaliana and Vibrio vulnificus MO6-24/O by RNA-seq |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In order to analyze the transcripts of Arabidopsis thaliana (Col-0) and Vibrio vulnificus MO6-24/O simultaneously, Vibrio vulnificus MO6-24/O was infiltrated onto Arabidopsis leaves and then leaves were harvested at 0, 3, 6, 12, 24 and 48 h post-infiltration. A total of 31, 128, 303, 219 and 130 differentially expressed genes (DEGs) of Vibrio were up- and down-regulated at 3, 6, 12, 24 and 48 h post-infiltration (hpi). Meanwhile, differentially expressed genes (DEGs) were monitored at 3, 6, 12, 24 and 48 h post-infiltration. A total of 2,097, 1,839, 1,220, 1,170 and 1,383 genes were characterized at each time points in Arabidopsis. Our data clearly indicate that total transcripts of the marine bacterial pathogen V. vulnificus MO6-24/O are detected and analyzed in plant Arabidopsis and two organisms were inter-communicated at the same time under favorable conditions.
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| Overall design |
Vibrio vulnificus MO6-24/O was infiltrated in Arabidiosps (Col-0) and then samples were harvested at 0, 3, 6, 12, 24 and 48 h. Negative control treated plants were also harvested at the same time points. Two samples were replicated at each time point. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq Stranded Total RNA LT (with Ribo-Zoro-Plant) Set A (Illumina, CA, USA) according to manufacturer’s protocols. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).
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| Contributor(s) |
Park Y, Park J, Ryu C |
| Citation(s) |
33995904 |
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| Submission date |
Oct 05, 2020 |
| Last update date |
May 19, 2021 |
| Contact name |
Yong-Soon Park |
| E-mail(s) |
[email protected]
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| Phone |
+82-10-9045-7454
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| Organization name |
Chungbuk National University
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| Department |
Biotechnology Research Institute
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| Street address |
Cheongju
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| City |
Cheongju-si |
| State/province |
Chungcheongbuk-do |
| ZIP/Postal code |
362763 |
| Country |
South Korea |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (24)
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| GSM4817420 |
Arabidopsis leaf infiltrated by PBS 0h-rep1 |
| GSM4817421 |
Arabidopsis leaf infiltrated by PBS 0h-rep2 |
| GSM4817422 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 0h-rep1 |
| GSM4817423 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 0h-rep2 |
| GSM4817424 |
Arabidopsis leaf infiltrated by PBS 3h-rep1 |
| GSM4817425 |
Arabidopsis leaf infiltrated by PBS 3h-rep2 |
| GSM4817426 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 3h-rep1 |
| GSM4817427 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 3h-rep2 |
| GSM4817428 |
Arabidopsis leaf infiltrated by PBS 6h-rep1 |
| GSM4817429 |
Arabidopsis leaf infiltrated by PBS 6h-rep2 |
| GSM4817430 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 6h-rep1 |
| GSM4817431 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 6h-rep2 |
| GSM4817432 |
Arabidopsis leaf infiltrated by PBS 12h-rep1 |
| GSM4817433 |
Arabidopsis leaf infiltrated by PBS 12h-rep2 |
| GSM4817434 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 12h-rep1 |
| GSM4817435 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 12h-rep2 |
| GSM4817436 |
Arabidopsis leaf infiltrated by PBS 24h-rep1 |
| GSM4817437 |
Arabidopsis leaf infiltrated by PBS 24h-rep2 |
| GSM4817438 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 24h-rep1 |
| GSM4817439 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 24h-rep2 |
| GSM4817440 |
Arabidopsis leaf infiltrated by PBS 48h-rep1 |
| GSM4817441 |
Arabidopsis leaf infiltrated by PBS 48h-rep2 |
| GSM4817442 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 48h-rep1 |
| GSM4817443 |
Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 48h-rep2 |
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| Relations |
| BioProject |
PRJNA667430 |
| SRA |
SRP286390 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE159018_RAW.tar |
3.1 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE159018_counts.txt.gz |
710.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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