|
| Status |
Public on Apr 27, 2022 |
| Title |
Wsm2+_WSMV_rep2 [XY2] |
| Sample type |
SRA |
| |
|
| Source name |
Homogenized whole leaf tissues
|
| Organism |
Triticum aestivum |
| Characteristics |
genotype: Wsm2+
treatment: WSMV treated
sample collection time: 10 days post inoculation on two week old seedlings
tissue: Homogenized whole leaf tissues
|
| Treatment protocol |
The WSMV treatment was prepared with 1:10 (w/v) dilution of the WSMV-infected wheat leaf tissue and 0.01 M potassium phosphate buffer (pH 7.4) and inoculated on two-week-old seedlings. The Buffer treatment were absent for WSMV infected tissues in the inoculum.
|
| Growth protocol |
Plants were grown in a Conviron PGR15 growth chamber at CSU, CO, in 12hr light/12hr dark conditions with a 18 °C day/ 15 °C night temperatures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from homogenized whole leaf tissues collected 10 days after inoculation using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
The Agilent 2100 bioanalyzer (RNA Nano Chip, Agilent, CA) was used to check RNA integrity. The library construction and sequencing via Illumina HiSeq 2000 were performed by Novogene Co., Ltd (Sacramento, CA, USA), approximately 150 bp paired end (PE) raw reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads of each paired-end library were examined for sequence quality and adaptor sequences were removed using Fastp with default settings
Trimmed paired-end RNA-seq reads were aligned to the reference genome using STAR 2.7.3 with parameters “-outFilterMismatchNmax 6 -alignIntronMax 10000”.
Non-normalized reads were counted with featureCounts (which is a function in subread-2.0.0) with parameters “-t gene -p” and used as input for the R package “DEseq2”
During the STAR 2.7.3 alignment, reads that did not map to IWGSC RefSeq v1.0 were collected with parameter “-outReadsUnmapped” and assembled with Trinity v2.10.0 using the following parameters: “-seqType fq –samples_file<input_file> -max_memory 10G -CPU 20”
Genome_build: Do novo assembly of unmapped reads
Supplementary_files_format_and_content: Raw counts of mapped reads
|
| |
|
| Submission date |
Dec 07, 2021 |
| Last update date |
Apr 27, 2022 |
| Contact name |
Yucong Xie |
| E-mail(s) |
leslieyx@colostate.edu
|
| Organization name |
Colorado State University
|
| Department |
Department of Soil and Crop Sciences
|
| Lab |
Pearce Lab
|
| Street address |
307 Campus delivery
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523 |
| Country |
USA |
| |
|
| Platform ID |
GPL17701 |
| Series (1) |
| GSE190382 |
Transcriptomic responses of common wheat segregating for Wsm2 locus to wheat streak mosaic virus (WSMV) and mock infection |
|
| Relations |
| BioSample |
SAMN23733489 |
| SRA |
SRX13341018 |
