|
Status |
Public on Jun 01, 2019 |
Title |
Mock_1dpi_25_rep3 |
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 |
SAMN10644900 |
SRA |
SRX5180528 |