|
| Status |
Public on Jun 01, 2019 |
| Title |
Mock_1dpi_25_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
inoculated leaf of 'PI152225'
|
| Organism |
Capsicum chinense |
| Characteristics |
dpi: 1
tissue: inoculated leaf
|
| Treatment protocol |
RNA samples were obtained from 1 and 5 dpi TSWV- and mock-inoculated PI152225 plants. To ensure that clear differences in resistance breakdown at different temperatures were detected, leaf samples with local necrosis were harvested at 5 dpi.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Inoculated leaves were extracted using RNA extraction kit(MG MED, Inc. Seoul, Korea)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQC v0.10.0 and trimmomatic (v0.36) for trimming illumina reads
Mapping using TopHat v2.0.13 with default options including parameter -p 8
DEG analysis were done by DESeq2 R package
FPKM value was obtained using TopHate 2 and cufflinks 2
Supplementary_files_format_and_content: comma (,) limited text files of DEGs in different conditions
|
| |
|
| Submission date |
Dec 26, 2018 |
| Last update date |
Jun 01, 2019 |
| Contact name |
JOUNGHO LEE |
| E-mail(s) |
shm97257@gmail.com
|
| Organization name |
Seoul National University
|
| Street address |
Gwanak-ro
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL25985 |
| Series (1) |
| GSE124386 |
RNA-Seq analysis sheds light on the breakdown of Tomato spotted wilt virus resistance in pepper at high temperature |
|
| Relations |
| BioSample |
SAMN10644901 |
| SRA |
SRX5180527 |
