|
| Status |
Public on Oct 26, 2023 |
| Title |
SR-N-3 |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
tissue: Seedlings
cell type: 7-day-old
genotype: sc106 -/-
treatment: 125 mM NaCl
|
| Treatment protocol |
Seeds are germinated on 125 mM NaCl, and mock.
|
| Growth protocol |
7-day-old seedlings
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Direct-zol RNA MiniPrep Plus (Zymo Research) according to the manufacturer’s instructions
The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol and sequenced on the NovaSeq platform to generate high-quality paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
High-quality RNA samples with RNA integrity number (RIN) 7.0 were selected for library construction. The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol.
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Trimming library adapters and quality controls with Trimmomatic using the following arguments; TrimmomaticPE - LEADING:25 TRAILING:25 CROP:120 MINLEN:120. Illumina adapters were removed and read pairs were trimmed to the same length
Alignement with STAR.
|
| |
|
| Submission date |
May 10, 2023 |
| Last update date |
Oct 26, 2023 |
| Contact name |
Haroon Butt |
| E-mail(s) |
[email protected]
|
| Phone |
00966542529194
|
| Organization name |
KAUST
|
| Department |
BESE
|
| Lab |
Laboratory for Genome Engineering and Synthetic Biology
|
| Street address |
King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900
|
| City |
Jeddah |
| State/province |
Makkah |
| ZIP/Postal code |
4700 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE232160 |
SCR106 splicing factor modulates abiotic stress responses by maintaining the RNA splicing in rice |
|
| Relations |
| BioSample |
SAMN35025269 |
| SRA |
SRX20277576 |
