|
| Status |
Public on Apr 24, 2023 |
| Title |
Mock_osfkbp20-1b_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
rice
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: Shoot
genotype: osfkbp20-1b mutant
treatment: mock
|
| Treatment protocol |
1-week-old rices were treated mock or ABA for 6 hours
|
| Growth protocol |
Rice seeds were sown on 1/2 MS gel for 3 days germination and transfer and growth the 50 mL conical ture 4 days in culture room (25℃, light/dart 16h/8h)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from leaf using WizPrepTM Plant RNA Mini Kit (WIZBIOsolutions, Seongnam, South Korea)
Total RNA was extracted from the leaves, and cDNA was synthesized using PrimeScript™ RT reagent Kit (TaKara, Japan). The resultant cDNA fragments were purifed, end-reparided, polyA-tailed, and ligated to index adapters following the Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing data were filtered using standard RNA-seq parameters (Illumina pipeline).
The transcriptome short reads (< 25 bp) were filtered out using DynamicTrim and LengthSort of solexaQA package
The read counts were calculated by mapping the filtered reads that passed the pre-processing using HTSeq
The filtered reads were normalised using the DESeq library
The IR ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons
The intron retention (IR) ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons. AS occurred outside of IRs requiring junction reads, junction information was extracted using regtools
Genome_build: IRGSP-1.0 (Oryza sativa Japonica Group (Japanese rice) genome assembly)
Supplementary_files_format_and_content: Xlsx was processed data
|
| |
|
| Submission date |
Feb 28, 2022 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Haemyeong Jung |
| E-mail(s) |
hmjung@kribb.re.kr
|
| Phone |
+82-10-3264-3931
|
| Organization name |
KRIBB
|
| Department |
Plant Systems Engineering Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE197599 |
Transcriptome analysis of alternative splicing under ABA exposure in osfkbp20-1b mutant compared to wild-type (ZH11) of rice |
|
| Relations |
| BioSample |
SAMN26311781 |
| SRA |
SRX14313597 |
