|
| Status |
Public on Sep 01, 2021 |
| Title |
C-4 leaf early stageEmbryo replicate-2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf early stageEmbryo
|
| Organism |
Triticum turgidum |
| Characteristics |
tissue: Embryo
Stage: leaf early stage
ecotype: CDC commander
|
| Treatment protocol |
Flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.
|
| Growth protocol |
Plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity was set to 100 to 120 μmol m−2 s−1 for whole life cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryo, endosperm and pericarp tissue isolation procedure were precisely performed as described in Xiang et al., 2019.
For RNA-seq profile analysis, Illumina mRNA-seq libraries were constructed using the TruSeq RNA kit (version 1, rev A).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
replicate-2
Rawcount.xlsx
|
| Data processing |
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads and eliminating short reads using Trimmomatic.
Filtered reads were mapped to the IWGSC RefSeq v2.0 assembly wheat genome using STAR.
Read counting was carried out with FeatureCounts.
Genome_build: IWGSC RefSeq v2.0 assembly wheat genome
Supplementary_files_format_and_content: Matrix table files include raw counts for each sample
|
| |
|
| Submission date |
Jun 28, 2020 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Peng Gao |
| E-mail(s) |
peng.gao@agr.gc.ca
|
| Organization name |
Agriculture and Agri-Food Canada
|
| Street address |
107 Science Place
|
| City |
Saskatoon |
| State/province |
Saskatchewan |
| ZIP/Postal code |
S7N 0X2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18539 |
| Series (1) |
| GSE153420 |
Gene profiles of Chinese Spring and CDC commander during embryogenesis |
|
| Relations |
| BioSample |
SAMN15395049 |
| SRA |
SRX8627642 |
