|
| Status |
Public on Oct 25, 2022 |
| Title |
S1_6 dpa Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
endosperm
|
| Organism |
Triticum turgidum subsp. durum |
| Characteristics |
tissue: endosperm
cultivar/variety: Kronos
genotype: WT
time: 6 dpa
|
| Growth protocol |
Plants were grown in controlled environment rooms (CERs) at 60% relative humidity with 16 h light at 20°C and 8 h dark at 16°C. The CER light intensity was 400 μmol photons m−2 s−1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted (n=3) from dissected endosperm tissue using the RNeasy PowerPlant kit (Qiagen).
Library preparation was carried out by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Kallisto version 0.46.1 to calculate TPM values and obtain estimated counts
DESeq2 to search for differentially expressed genes
Assembly: Triticum turgidum Svevo.v1 canonical transcripts
Supplementary files format and content: tab-delimited text files include TPM values for each sample
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Oct 25, 2022 |
| Contact name |
Martin Vickers |
| E-mail(s) |
martin.vickers@jic.ac.uk
|
| Organization name |
John Innes Centre
|
| Street address |
Colney Ln
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL28728 |
| Series (1) |
| GSE216253 |
Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis |
|
| Relations |
| BioSample |
SAMN31394206 |
| SRA |
SRX17979162 |
