|
Status |
Public on Oct 26, 2023 |
Title |
WT-N-3 |
Sample type |
SRA |
|
|
Source name |
Seedlings
|
Organism |
Oryza sativa Japonica Group |
Characteristics |
cultivar: Nipponbare tissue: Seedlings cell type: 7-day-old genotype: WT 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) |
haroon.butt.1@kaust.edu.sa
|
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 |
SAMN35025263 |
SRA |
SRX20277582 |