|
| Status |
Public on Sep 03, 2019 |
| Title |
Wild-type seedling shoots |
| Sample type |
SRA |
| |
|
| Source name |
Seedling shoots
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar/ecotype: Nipponbare (NIP)
developmental stage: Two-week-old
genotype/variation: wild type
tissue: Seedling shoots
|
| Treatment protocol |
N/A
|
| Growth protocol |
The seeds of all rice materials were sowed in early June in the paddy field on natural condition in Hangzhou of the year 2017, and then the materials were sampled at indicated times
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with RNAprep pure Plant kit (TIANGEN, Cat. no. DP432).
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NIP-shoot
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with SOAPnuke1.3.0; Clean reads were aligned to reference genomes (TIGR release 7) using Hisat2 with default parameters.
Mapped reads from three biological replicates for rice were merged and then assembled with Cufflinks (v2.2.1).
Genome_build: Rice TIGR release 7
Supplementary_files_format_and_content: FPKM and Annotation of DEGs as indicated in the file name
|
| |
|
| Submission date |
May 15, 2019 |
| Last update date |
Sep 03, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
jkzhu@sibs.ac.cn
|
| Organization name |
Shanghai Center for Plant Stress Biology
|
| Street address |
No. 3888 Chenhua Road
|
| City |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL19290 |
| Series (1) |
| GSE131243 |
The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice |
|
| Relations |
| BioSample |
SAMN11653441 |
| SRA |
SRX5833593 |
