|
| Status |
Public on Mar 24, 2021 |
| Title |
OsGRP3 KD_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
rice leaf
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype: OsGRP3 Knock-down
growth stage: 4-week-old
cultivar: Dongjin
tissue: leaf
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Rice plants were grown in soil for 4 weeks at 28 °C with a cycle of 16 h light/ 8 h dark having light intensity of 200 µmol m-2 s-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4-week-old rice leaves were ground with liquid nitrogen, and total RNA was extracted using Rneasy plant mini kit (Qiagen). Illumina TruSeq mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to IRGSP-1.0 whole genome using HISAT2 through bowtie2 aligner
Gene/transcript was assemblied using reference gene model by StringTie program. Trancript abundance measurement was calculated by read count and FPKM value.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Gtf files by Stringtie include FPKM values for each Sample.
|
| |
|
| Submission date |
May 28, 2020 |
| Last update date |
Mar 24, 2021 |
| Contact name |
Jun Sung Seo |
| E-mail(s) |
[email protected]
|
| Organization name |
LaSemilla Co. Ltd.
|
| Department |
Company-affiliated research institute
|
| Street address |
Pyeongchangdaero 1447
|
| City |
Pyeongchang |
| State/province |
Gangwon |
| ZIP/Postal code |
25354 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE151351 |
Genome-wide transcriptome analysis between WT and OsGRP3 overexpressing (or knock-down) rice |
|
| Relations |
| BioSample |
SAMN15044376 |
| SRA |
SRX8413192 |
