|
| Status |
Public on Jan 31, 2023 |
| Title |
Leaf_rep3_CSPh1b |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue/stage: Leaf
genotype: Chinese Spring CSPh1b
process: Ph1b mutant
|
| Treatment protocol |
Plants were treated every two weeks using water soluble 20-20-20 fertilizer at a rate of 3.0 g L-1 and chelated micronutrient mix at a rate of 0.3 g L-1
|
| Growth protocol |
Plants were grown in a growth chamber at aconstant temperature of 21±1°C, a photoperiod of 16 h day and 8 h night and the minimum photosynthetic photon flux density of 400 μmol m−2 s−1 during the day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Meiocytes were isolated using MioCapture protocol (Shunmugam et al. 2018 BMC Plant Biology 18: 293)
TruSeq RNA sequencing libraries were constructed following the manufacturer’s instructions (Illumina, http://www.illumina.com/)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Short Illumina reads were filtered using Trimmomatic by trimming adapter and low quality sequences and removing reads shorter than 75 bp
Filtered reads were aligned to the wheat reference genome (IWGSC v1.0) using STAR
Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and the expected read counts and transcripts per million (TPM) values were generated
Genome_build: IWGSCv1.0
Supplementary_files_format_and_content: Matrix table with TPM values for each sample
Supplementary_files_format_and_content: Matrix table with readcounts values for each sample
|
| |
|
| Submission date |
Aug 16, 2021 |
| Last update date |
Jan 31, 2023 |
| Contact name |
Sateesh Kagale |
| E-mail(s) |
Sateesh.Kagale@nrc-cnrc.gc.ca
|
| Organization name |
National Research Council Canada
|
| Department |
Aquatic and Crop Resource Development
|
| Street address |
110 Gymnasium Place
|
| City |
Saskatoon |
| State/province |
SK |
| ZIP/Postal code |
S7N 0W9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18862 |
| Series (1) |
| GSE182171 |
Dynamic coding and noncoding RNA interactions coordinate gene expression during meiosis in wheat |
|
| Relations |
| SRA |
SRX11765728 |
| BioSample |
SAMN20835177 |
