|
| Status |
Public on Feb 01, 2023 |
| Title |
BI2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf whorl tissue
|
| Organism |
Triticum aestivum |
| Characteristics |
cultivar: resistant (Byrd)
tissue: leaf whorl
treatment: wheat curl mite
|
| Treatment protocol |
At 14 days after planting, wheat plants were checked for uniformity in phenotypic growth and health before being used for WCM infestation. The study was conducted as a randomized complete block design with a factorial arrangement of treatments consisting of two wheat varieties (WCM-resistant and WCM-susceptible) and two WCM treatments (infested and non-infested). For each treatment, three replicates were used, and for each treatment, a replicate consisted of three individual wheat plants
|
| Growth protocol |
Seeds were planted individually in cone-tainers (4 cm top diameter and 20 cm length) with standard greenhouse mix. These cone-tainers (Steuwe and Sons Inc., Corvallis, Oregon, USA) were covered with tube cages and kept in the growth chamber with 14:10 (L:D) photoperiod at 25oC and ca. 60% relative humidity. Cages were made from clear cylindrical plastic tubes (5 cm diameter and 50 cm length), vented with three 5-cm diameter openings covered with Nitex® screen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Wheat whorl tissues (80-100 mg) were ground using 2010 Geno/Grinder® (SPEX SamplePrep, NJ, USA) for 40 seconds at 1400 strokes min-1. Total RNA was extracted from the homogenized tissue using the kit NucleoSpin miRNA for miRNA and RNA purification (Macherey-Nagel, NucleoSpin miRNA, Mini kit for miRNA and RNA purification, ref 740971.50)
mRNA-seq libraries were constructed following the Illumina TruSeq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Trimming: Trimmomatic v0.39
Mapping: Tophat2
Differential expression analysis: Cuffdiff v2.2.1
Genome_build: Chinese Sping v2.1
Supplementary_files_format_and_content: Matrix table with gene FPKM for every gene and every sample
|
| |
|
| Submission date |
Feb 02, 2022 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Lise Pingault |
| E-mail(s) |
lise.pingault@unl.edu
|
| Phone |
4059854042
|
| Organization name |
University of Nebraska-Lincoln
|
| Street address |
1700 East Campus Mall, 312F Entomology Hall
|
| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68583 |
| Country |
USA |
| |
|
| Platform ID |
GPL25409 |
| Series (1) |
| GSE195958 |
Wheat transcriptomic responses to long-term feeding by wheat curl mites |
|
| Relations |
| SRA |
SRX12293410 |
| BioSample |
SAMN21552663 |
