|
| Status |
Public on May 16, 2014 |
| Title |
R9308-12 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Root
|
| Organism |
Oryza sativa |
| Characteristics |
strain: cv.R9308
tissue: root
developmental stage: Tillering stage
|
| Growth protocol |
Rice seeds were surface-sterilized with 3% H2O2 for 10 min and then rinsed with distilled water several times. After soaking in distilled water at 37℃ for 2d, germinated seeds were sowed in the field of the China National Rice Research Institute, Fuyang, China, for approximately 30 d. Then 40 seedlings of each genotype were transplanted in plots on a floating foamed plastic in a pool full of nutrient solution. Roots were sampled with ten replicates at the tillering stage and heading stage to measure root traits and estimate heterosis. Meantime, for RNA-Seq analysis, two roots of every genotype at either stage were collected and stored at -80℃ before use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from roots using TRIzol regent (Invitrogen) and purified with Oligotex mRNA Midi Kit (QIAGEN). RNA quality was checked by the Bioanalyzer 2100 (Aligent) and all samples had RNA Integrity Number (RIN) value more than 8.5. The sequencing library was prepared according to manufacturer′s instructions (Illumina). The poly-A containing mRNA was isolated from total RNA using two rounds of purification with poly-T oligo-attached magnetic beads and subsequently fragmented by the RNA fragmentation kit. The first strand cDNA was generated using reverse transcriptase and random primers. After the second strand cDNA synthesis and adaptor ligation, cDNA fragments of 200 bp were isolated by gel electrophoresis and enriched by 18 cycles of PCR. The products were loaded on Illumina Hiseq2000 instrument for pair-end 100 bp×2 sequencing for 100 cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
The raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 30% Q<20 bases. Then the low-quality bases (Q<20) at the 5’ and 3’ ends of the remaining reads were discarded.
Sequences were mapped onto the Nipponbare reference genome using Stampy (v1.0.13). Single nucleotide polymorphisms (SNPs) were called using the Samtools (v. 0.1.16) .
Supplementary_files_format_and_content: text file include SNPs for each Sample ...
|
| |
|
| Submission date |
Jan 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rongrong Zhai |
| E-mail(s) |
fy_555500@163.com
|
| Organization name |
China National Rice Research Institute
|
| Street address |
No. 359, Tiyuchang Rd
|
| City |
hangzhou |
| ZIP/Postal code |
310006 |
| Country |
China |
| |
|
| Platform ID |
GPL13160 |
| Series (1) |
| GSE43727 |
Identification of transcriptome SNPs for assessing allele specific gene expression within a super-hybrid rice Xieyou9308 |
|
| Relations |
| SRA |
SRX219960 |
| BioSample |
SAMN01902561 |
