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| Status |
Public on Oct 06, 2019 |
| Title |
Gene expression profiling study by RNA-seq in Arabidopsis thaliana infected by Vibrio vulnificus |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The objective of this study is to assess gene expression changes in Arabidopsis thaliana as time passed after Vibrio vulnificus 96-11-17M infection. We performed transcript profiling using 10 RNA-seq samples of Arabidopsis obtained at 0h, 12h, 24h, 48h, and 72h after 96-11-17M treatment. Through various statistical tests, differentially expressed genes at each time point were obtained and enriched biological functions were compared across infection time points. Many enriched functions associated with immune or defence systems of plant were common in all infection times. Compared with other gene expression data sets infected by several plant pathogens, common activated genes were small, but similar biological functions were shared between Vibrio and plant pathogen infections.
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| Overall design |
RNA-seq data of 10 samples were generated at 5 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 RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).
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| Contributor(s) |
Kim J, Kim S, Kim S, Park Y, Ryu C |
| Citation(s) |
31841567 |
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| Submission date |
Sep 15, 2014 |
| Last update date |
Jan 05, 2020 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
[email protected]
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| Phone |
+82-42-879-8107
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| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
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| Department |
Personalized Genomic Medicine Research Center
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| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
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| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (10)
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| GSM1504314 |
Arabidopsis leaf infected by 96-11-17M 0h rep 1 |
| GSM1504315 |
Arabidopsis leaf infected by 96-11-17M 0h rep 2 |
| GSM1504316 |
Arabidopsis leaf infected by 96-11-17M 12h rep 1 |
| GSM1504317 |
Arabidopsis leaf infected by 96-11-17M 12h rep 2 |
| GSM1504318 |
Arabidopsis leaf infected by 96-11-17M 24h rep 1 |
| GSM1504319 |
Arabidopsis leaf infected by 96-11-17M 24h rep 2 |
| GSM1504320 |
Arabidopsis leaf infected by 96-11-17M 48h rep 1 |
| GSM1504321 |
Arabidopsis leaf infected by 96-11-17M 48h rep 2 |
| GSM1504322 |
Arabidopsis leaf infected by 96-11-17M 72h rep 1 |
| GSM1504323 |
Arabidopsis leaf infected by 96-11-17M 72h rep 2 |
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| Relations |
| BioProject |
PRJNA261035 |
| SRA |
SRP047128 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61418_RAW.tar |
1.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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