|
| Status |
Public on Dec 19, 2024 |
| Title |
PP_stock_21_2 |
| Sample type |
SRA |
| |
|
| Source name |
Stock
|
| Organism |
Capsicum annuum |
| Characteristics |
time: 21 DAG
tissue: Stock
|
| Treatment protocol |
A 0.5 cm of tomato:tomato, pepper:pepper, tomato:pepper, and pepper tomato scion and stock were collected at 7, 14, and 21 days after grafting. Ungrafted tomato and pepper stems of the same age were also collected for tomato and pepper. Each sample had between 3-5 bioreplicates.
|
| Growth protocol |
Solanum lycopersicum var. M82 (tomato) and Capsicum annuum var. California Wonder(pepper) seeds were straitified with 50% bleach. Tomato seeds were germinated in moist phytatrays and pepper seeds were germinated on soil on heatmaps. Tomato and pepper seedlings were grown in climate-controlled chambers set to 23 C with 16:8 day/night light cycles. 21 day old pepper and 14 day old tomato seedlings were grafted and allowed to heal in the dark for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was flash frozen and hand ground with a mortal and pestle. Total RNA was purified from Trizol-extracted samples using the Monarch Total RNA Miniprep Kit.
Libraries were built by the Cornell Institute of Biotechnology, Biotechnology Resource Centre using the Lexogen QuantSeq FWD prep kit and Poly(A) RNA Selection Kit V1
5 and subjected to high-throughput sequencing with the Illumina NextSeq 500/550 High-output kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
pepper_gene_count_matrix_final.csv
|
| Data processing |
Fasta files were quality checked using FastQC 0.12.1.
TruSeq3 adaptors trimmed with Trimmomatic v0
39 with a head crop setting of 12, trailing setting of 3, minimum length of 52, and a sliding window of 4:20
The polyA tail was trimmed using Prinseq v0.20.4 with the left and right tail length (i.e. trim_trail_left) of 8 and the minimum length of 40.
Genome indexes were built for tomato and pepper using the ITAG4 and CM334 models respectively. Reads were aligned using STAR 2.7.10b with two pass mode.
Files were sorted using Samtools 1.18.
Files were assembled using Strintie version 2.2.1.
Assembly: ITAG4.0 4081, Capsicum annuum 4072
Supplementary files format and content: raw reads matrix file for tomato and pepper
|
| |
|
| Submission date |
Feb 19, 2024 |
| Last update date |
Dec 19, 2024 |
| Contact name |
Hannah Rae Thomas |
| E-mail(s) |
hannah.thomas@jic.ac.uk
|
| Organization name |
John Innes Centre
|
| Department |
Cell and Developmental Biology
|
| Lab |
Christine Faulkner
|
| Street address |
Norwich Research Park, Colney Lane
|
| City |
Norwich |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL34211 |
| Series (1) |
| GSE256079 |
Cell death at the Solanum lycopersicum and Capsicum graft junction is due to genetic incompatibility |
|
| Relations |
| BioSample |
SAMN39991865 |
| SRA |
SRX23662918 |
