|
| Status |
Public on Jan 13, 2016 |
| Title |
LS |
| Sample type |
SRA |
| |
|
| Source name |
Leaf_salt stressed
|
| Organism |
Oryza rufipogon |
| Characteristics |
genotype/variation: Dongxiang wild rice
developemental stage: seedling stage
tissue: leaf
exposed to: 200 mM NaCl solution for 3 days
|
| Treatment protocol |
After the seedlings had been grown for 14 days, they were transferred on their 96-well plates into containers filled with 200 mM NaCl solution, or with control solution for 3 days.
|
| Growth protocol |
Seeds of Dongxiang wild rice (Oryza rufipogon Griff.) were immersed in distilled water in the dark, and the uniformly germinated seeds were sown in 96-well plates supported by a plastic container. Seeds were grown in a growth chamber and the growth culture solution was renewed every 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted for the three biological replicates from the sampled leaf or root tissues collected from the three seedlings for each biological replicate using the TRIzol kit following the manufacturer’s instructions (Invitrogen).
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 50% Q<10 bases. Then the low-quality bases (Q<10) at the 5’ and 3’ ends of the remaining reads were discarded. Passed filter reads were mapped onto the Nipponbare reference genome (IRGSP build 5.0)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated to detect gene expression levels.
Genome_build: Nipponbare reference genome (IRGSP build 5.0)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Sep 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yi Zhou |
| E-mail(s) |
[email protected]
|
| Organization name |
Jiangxi Normal University
|
| Street address |
No. 99, Ziyang Rd
|
| City |
Nanchang |
| State/province |
Jiangxi |
| ZIP/Postal code |
330022 |
| Country |
China |
| |
|
| Platform ID |
GPL15800 |
| Series (1) |
| GSE73181 |
Transcriptome analysis of salt stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.) |
|
| Relations |
| BioSample |
SAMN04095795 |
| SRA |
SRX1258046 |
