|
| Status |
Public on Jan 08, 2024 |
| Title |
Cell, Chitin 2, 6 h |
| Sample type |
SRA |
| |
|
| Source name |
suspension cell
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cell type: suspension cell
genotype: WT
treatment: chitin
|
| Treatment protocol |
Add chitin at a final concentration of 2 µg/mL, and harvest the samples at 0, 1, 3, 6, and 12 h.
|
| Growth protocol |
Grow rice suspension cells in a flask on a shaker at 50 rpm at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA is extracted with a TRIzol reagent according to the manufacturer’s instructions.
Quantify RNAs with a Qubit RNA HS Assay Kit, and examine their integrity using a Bioanalyzer 2100. Use RNA samples with RIN > 7 for library preparation with the TruSeq Stranded mRNA LT Sample Prep Kit following the manufacturer's protocol. Libraries were sequenced to generate paired-end 150-bp reads on a Hiseq2500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rice (Oryza sativa L. subsp. japonica cv. Nipponbare)
|
| Data processing |
Check the quality of sequencing data with FastQC. Filter the low-quality base pairs (Q < 17) in the raw sequencing data with DynamicTrim, a program in SolexaQA
Remove the reads less than 25 bp with LengthSort in SolexaQA.
Remove adapter sequences with Cutadapt
Map clean reads to the rice genome (MSU7) using hisat2 with default parameters and the following adjustments: -p 28, which means using 28 threads to improve computational speed
Assembly: Map clean reads to the rice genome (MSU7) using hisat2
Supplementary files format and content: Include rawcounts for each sample
|
| |
|
| Submission date |
Jan 08, 2024 |
| Last update date |
Jan 09, 2024 |
| Contact name |
Yoji Kawano |
| E-mail(s) |
yoji.kawano@okayama-u.ac.jp
|
| Organization name |
Okayama University
|
| Department |
Institute of Plant Science and Resources
|
| Street address |
2-20-1, Chuo
|
| City |
Kurashiki |
| State/province |
Okayama |
| ZIP/Postal code |
710-0046 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18525 |
| Series (2) |
| GSE252767 |
Identification of endogenous small peptides involved in rice immunity through transcriptomics- and proteomics-based screening |
| GSE252769 |
Identification of endogenous small peptides involved in rice immunity through transcriptomics- and proteomics-based screening |
|
| Relations |
| BioSample |
SAMN39305681 |
| SRA |
SRX23135315 |
