|
| Status |
Public on Aug 21, 2023 |
| Title |
CM-TDW_1D-1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Capsicum annuum |
| Characteristics |
tissue: Leaves
genotype: WT
treatment: P.infestans_Mock
timepoint: 1D
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
replicate1
|
| Data processing |
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Aug 21, 2023 |
| Contact name |
Seon-In Yeom |
| E-mail(s) |
[email protected]
|
| Organization name |
Gyeongsang National University
|
| Street address |
501, Jinjou-daero
|
| City |
Jinju |
| ZIP/Postal code |
52828 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26789 |
| Series (2) |
| GSE240945 |
The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA385363] |
| GSE240949 |
The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper |
|
| Relations |
| BioSample |
SAMN06227033 |
| SRA |
SRX2782758 |
