|
| Status |
Public on Jun 20, 2020 |
| Title |
resistant.control.day1.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Capsicum annuum |
| Characteristics |
tissue: root
group: resistant
agent: none
time point: day1
|
| Treatment protocol |
The treatment plants were inoculated with 300 Meloidogyne incognita juveniles
|
| Growth protocol |
The plants were grown in 100% sand, and watered daily
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The whole root of the plants were extracted use Qiagen's plant mini RNA extraction kit
whole RNA was prepared following standard Illumina Hiseq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
resistant control day1 rep1
CC11
|
| Data processing |
Raw sequences were checked for quality using FastQC
reads with a quality score above 30 were aligned directly to the pepper reference genome Capsicum annuum vision 1.55 utilizing the program STAR
Gene counts were summarized by HTSeq-count, Differentially Expressed Genes (DEG) were calculated using R package “DESeq2”
The number of DEG shared across time points and treatments was calculated in R, and Venn diagram plots were generated using Venny2.1
Genome_build: capsicum annuum vision 1.55
Supplementary_files_format_and_content: processed data were stored in tab file, including the normalized abundance measurements of all samples
|
| |
|
| Submission date |
Jun 19, 2020 |
| Last update date |
Jun 20, 2020 |
| Contact name |
Weiming Hu |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Florida
|
| Department |
Entomology and Nematology
|
| Street address |
1881 Natural Area Dr.
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32608 |
| Country |
USA |
| |
|
| Platform ID |
GPL26789 |
| Series (1) |
| GSE152857 |
A Comprehensive Transcriptional Profiling of Pepper Responses to Root Knot Nematode |
|
| Relations |
| BioSample |
SAMN15327065 |
| SRA |
SRX8584337 |
