|
| Status |
Public on Nov 28, 2022 |
| Title |
AK58_Root_RNA-seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Triticum aestivum 2-weeks-old seedlings
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: roots
cultivar: AiKang58
|
| Treatment protocol |
The three tissues of wheat, including leaves, roots and shoot apices, were obtained after 2 weeks of growth. The 2-week-old seeding were vernalized at 4°C under 16h light/8h dark conditions for 30 days and 1.0 - 2.0 cm axillary buds were obtained from these vernalized seedings.
|
| Growth protocol |
16h light 22°C, 8h dark 19°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA
For each sample, total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit (Illumina, San Diego, CA) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed with Trimmomatic v0.334 with default parameters. The remaining reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using HISAT2 v2.0.5. Gene expression values were computed using StringTie v1.3.3b.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: TPM values for each sample
|
| |
|
| Submission date |
Nov 12, 2021 |
| Last update date |
Nov 28, 2022 |
| Contact name |
Zefu Lu |
| E-mail(s) |
luzefu@live.com
|
| Organization name |
Institute of Crop Sciences
|
| Street address |
No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China
|
| City |
Beijing |
| State/province |
Haidian |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL25409 |
| Series (2) |
| GSE188723 |
Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [RNA-seq] |
| GSE188724 |
Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat |
|
| Relations |
| BioSample |
SAMN23098946 |
| SRA |
SRX13124190 |
