|
| Status |
Public on Feb 14, 2017 |
| Title |
well-watered control |
| Sample type |
SRA |
| |
|
| Source name |
5-week old wild type rice
|
| Organism |
Oryza sativa |
| Characteristics |
ecotype: Illmi
tissue types: leaves
tissue age: 5 weeks
|
| Treatment protocol |
Multiple pots of each rice were divided into 2 sets, one for drought and one for well-watered treatment conditions. Five weeks after transplanting to soil, water was withheld, and the soil water content in each pot was adjusted to approximately 75%. Soil moisture was monitored during the drought treatment using a Soil Moisture Sensor SM150 (Delta-T Devices, UK)
|
| Growth protocol |
Rice was germinated on MS media at 28C for 4 days, and transplanted into soil pots and grown in a greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from rice leaves using Trizol reagent (Invtrogen) and purified an RNeasy Mini Kit (Qiagen).
A modified TruSeq method was used to construct strand-specific RNA-seq libraries with differnet ibdex primers.
barcode: ATCACG
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
control leaves
|
| Data processing |
Single-end seq were generated and raw seq reads were trimmed to removed adaptor seq, and those with a quality lower than Q20 were removed using the clc quality trim software (CLCBIO).
Duplicate paired short reads were removed using FastUniq.
All reads were assembled with the clc_ref_assmble 6 (version 4.06) program, using annotated gene and noncoding RNA seq from the rapdb (http://rapdb.dna.affrc.go.jp) and ncRNA (http://www.ncrna.org) databases.
genome_build: IRGSP-1.0
|
| |
|
| Submission date |
Apr 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pil Joong Chung |
| E-mail(s) |
[email protected]
|
| Organization name |
Seoul National University
|
| Department |
Crop Biotechnology Institute
|
| Lab |
Crop Biotechnology Lab
|
| Street address |
Pyeongchang daero 1447
|
| City |
Pyeongchang |
| State/province |
Gangwondo |
| ZIP/Postal code |
232-916 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19290 |
| Series (1) |
| GSE80811 |
Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice |
|
| Relations |
| BioSample |
SAMN04915024 |
| SRA |
SRX1736751 |
