|
| Status |
Public on Jul 14, 2023 |
| Title |
dsHR96-LBD-1 on tomato rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Tetranychus urticae |
| Characteristics |
tissue: whole organism
genotype: Near isogenic line B-NIL-HS1(RR)
treatment: Grown on tomato (Solanum lycopersicum) as host plant, injection with dsHR96-LBD-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using IlluminaTruseq stranded mRNA library prep (carried out at Fasteris, Switzerland)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to the genome with STAR (version 2.7.3a)
BAM files were sorted with samtools (version 1.9).
Raw read counts were obtained with htseq-count (version 2.0.1) using the Tetranychus_urticae_2022_12 genome annotation.
Assembly: Bulk segregant analysis scaffolded Tetranychus urticae reference genome reported by Wybouw et al. 2019 (GENETICS; 211: 1409–1427: doi: 10.1534/genetics.118.301803).
Supplementary files format and content: Processed data files consist of raw read counts per sample (from htseq-count output).
|
| |
|
| Submission date |
Dec 23, 2022 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Marilou Vandenhole |
| E-mail(s) |
marilou.vandenhole@ugent.be
|
| Phone |
0032478351164
|
| Organization name |
UGent
|
| Department |
Department of Plants and Crops
|
| Lab |
Lab of Agrozoölogy
|
| Street address |
Coupure links 653
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL28937 |
| Series (1) |
| GSE221677 |
Expression quantitative trait locus (eQTL) mapping with a cross between Tetranychus urticae inbred strains MR-VPi and ROS-ITi |
|
| Relations |
| BioSample |
SAMN32387408 |
| SRA |
SRX18839530 |
