|
| Status |
Public on Dec 27, 2023 |
| Title |
C92_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
14-day-old seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: C92
tissue: Shoot
age: 14 days
|
| Growth protocol |
Rice cultivar C92, MH63 and their hybrid were used for all experiments in this study. Seeds were grown in water under long-day conditions (16-h light at 28°C and 8-h dark at 28°C) in a growth chamber (100 μmol·m-2·s-1) for 2 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen) and treated with RNase-free DNase I (Promega) to remove any contaminating genomic DNA.
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the standard Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PolyA RNA isolated
|
| Data processing |
C92 and MH63 RNA-seq reads were mapped to the corresponding assembled genomes, respectively, using HISAT2 (version 2.0.5) software with default parameters (Kim et al. 2015). Reads that can map to multiple position were discarded before subsequent analyses. For F1 hybrid, we aligned RNA-seq reads to both of the parental genomes. We then split F1 RNA-seq reads into reads that can mapped to both of the parental genomes (common reads) or only to one of the genome (allele reads) based upon the highest quality alignment. Both of the common reads and allele reads were used to calculation mRNA expression levels in F1 hybrid.
Genome_build: MSU 7.0 (http://rice.plantbiology.msu.edu)
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Dec 30, 2019 |
| Last update date |
Dec 27, 2023 |
| Contact name |
Xuncheng Wang |
| E-mail(s) |
1706380435@pku.edu.cn
|
| Organization name |
Peiking University
|
| Street address |
5 Yiheyuan Road
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE142770 |
Genetic selection shaped the gene expression patterns of mRNA and protein in rice subspecies |
|
| Relations |
| BioSample |
SAMN13701730 |
| SRA |
SRX7480524 |
