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| Status |
Public on Apr 20, 2019 |
| Title |
Expression of defense related genes in resistance and susceptible tobacco (Nicotiana tabacum) in response to Ralstonia solanacearum infection |
| Organism |
Nicotiana tabacum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Comparative transcriptome analysis was performed to study gene expression profiles in resistant (Yanyan 97, YY97, 25) and susceptible (Huanghuadajinyuan, HD, 36) tobacco in responding to Ralstonia solanacearum infection. Illumina sequencing yielded a total of 67,619,833,668 bases data, and about 223.99 M and 223.82 M raw reads for Hd and Yy97 plants, respectively. About 209.73 M and 209.18 M clean reads of Hd and Yy97 were mapped to reference genome via Hisat2, respectively. The ratio of mapped clean reads for eight libraries ranged from 93.92% to 96.67% (average: 95.9%). By comparing gene expression levels in Rs infected and control tobacco stems, we identified 15374 DEGs in Hd plants after Rs infection, which included 7220 up-regulated and 8154 down-regulated DEGs. We identified 2120 DEGs in Yy97 plants after Rs infection, which included 1794 up-regulated and 326 down-regulated DEGs.
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| Overall design |
Stem samples of Ralstonia solanacearum infested(tm) and un-infested (ck) tobacco were RNA-Seq sequenced to compare differentially expressed genes.
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| Contributor(s) |
Zhang Y, Yu Y, Guo B |
| Citation missing |
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| Submission date |
Apr 20, 2018 |
| Last update date |
Apr 20, 2019 |
| Contact name |
Yongting Yu |
| Organization name |
Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science
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| Street address |
No 348, Xianjiahu West Rd.
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| City |
Changsha |
| ZIP/Postal code |
410205 |
| Country |
China |
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| Platforms (1) |
| GPL22345 |
Illumina HiSeq 2500 (Nicotiana tabacum) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA451198 |
| SRA |
SRP141439 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE113473_Assembled_unigene.fa.gz |
55.7 Mb |
(ftp)(http) |
FA |
| GSE113473_hd_geneExpression.txt.gz |
8.0 Mb |
(ftp)(http) |
TXT |
| GSE113473_yy97_geneExpression.txt.gz |
7.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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