|
| Status |
Public on Mar 25, 2022 |
| Title |
CR3 |
| Sample type |
SRA |
| |
|
| Source name |
Control (root)
|
| Organism |
Solanum lycopersicum |
| Characteristics |
var.: marmande
tissue: Root
treatment: Control
|
| Treatment protocol |
Tomato seeds were coated with Artemissia Absinthium essential oil (AEO) and inoculated with Fusarium oxysporum sp. Oxysporum radicis lycopersici, data were collected after 12 days
|
| Growth protocol |
Hydroponic culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Real Time Analysis software (RTA) used for basecalling.
PCR duplicates are removed using Cutadapt software.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Know genes and transcripts are assembled with StringTie with aligned reads based on reference genome model (SL2.50).
Read count is calculated using featureCounts function from Bioconductor
Genome_build: SGN release version SL2.50
Supplementary_files_format_and_content: Matrix table with raw gene reads counts for every gene and every sample
|
| |
|
| Submission date |
Oct 28, 2021 |
| Last update date |
Mar 25, 2022 |
| Contact name |
Marta Berrocal-Lobo |
| E-mail(s) |
m.berrocal@upm.es
|
| Organization name |
School of Forestry Engineering and Natural Resources
|
| Department |
System and Natural Resources
|
| Street address |
Antonio Nováis 10, s/n
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL25655 |
| Series (1) |
| GSE186754 |
RNA sequencing of tomato seedlings infected with Fusarium responding to an Artemissia Absinthium essential oil |
|
| Relations |
| BioSample |
SAMN22636300 |
| SRA |
SRX12812370 |
