|
| Status |
Public on Aug 21, 2017 |
| Title |
PR Uninfected Stage 1 rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole roots
|
| Organisms |
Solanum lycopersicum; Meloidogyne incognita |
| Characteristics |
control or experimental sample: Control
tissue: roots
tomato cultivar: Pusa Ruby
tomato susceptibility to root-knot nematode infection: susceptible
days post rkn inoculation: 1,2,3 days post inoculation
disease developmental stage: No disease
|
| Treatment protocol |
Five-week old tomato seedlings were inoculated with 1500 freshly hatched J2s per plant and water (control) in black potted trays. Whole roots at different days post infection (dpi) were collected with two to five technical replicates.
|
| Growth protocol |
Tomato seeds were germinated in trays (36cm x 25cm x 7cm) in sterile soil:solrite (1:4) at 22±2ºC, 16h light/8h dark cycle in greenhouse chamber. Three week old seedlings were transferred to black potted trays (4cm in diameter) in soil:sand (1:1). Stocks of Meloidogyne incognita were maintained on susceptible tomato and brinjal plants in a greenhouse culture room. Infected roots were collected; egg masses were hand-dissected and kept in autoclaved double distilled water for hatching at room temperature.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction protocol not provided.
Transcriptome libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina, USA) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PR_UI_123
|
| Data processing |
Basecalling was performed using CASAVA version 1.8
Quality assessment was carried out using FastQC and quality filtering of raw reads was done for mean phred quality score of 20 and any contaminating adapter sequences were removed using PrinSeq and Cutadapt.
After filtering for the good quality reads, reads were aligned independently onto S. lycopersicum and M. Incognita genomes using TopHat v2.0.14 on default parameters.
After alignment, uniquely mapped reads were further quantified using HTSeq based on gene annotations.
Genome_build: S. lycopersicum genome build SL2.50; M. Incognita WB release 5 (http://parasite.wormbase.org/). The gene annotations are publicly available at: http://parasite.wormbase.org/Meloidogyne_incognita_prjea28837/Info/Index/
Supplementary_files_format_and_content: bigWig files for each sample; tab-delimited text files include read count values for each Sample.
|
| |
|
| Submission date |
Oct 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Neha Shukla |
| E-mail(s) |
nehashukla04@gmail.com
|
| Organization name |
CEITEC
|
| Department |
Plant Molecular Biology
|
| Street address |
Kamenice 753
|
| City |
Brno |
| ZIP/Postal code |
62500 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL22563 |
| Series (1) |
| GSE88763 |
Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both plant and nematode during susceptible and resistance responses. |
|
| Relations |
| BioSample |
SAMN05908682 |
| SRA |
SRX2245668 |
