|
| Status |
Public on Dec 15, 2020 |
| Title |
IR64_N+W+_shoot |
| Sample type |
SRA |
| |
|
| Source name |
Shoot
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: IR 64
tissue: Shoot
growth stage: Seedling
stress: No stress
|
| Treatment protocol |
Wherever nitrogen stress has to be imposed, 0.4 mM ammonium nitrate was supplied; otherwise 0.08 mM ammonium Nitrate was supplied. Simialrly water stress was imposed on 15 day old seelings by limited water supply (10 ml) against 100 ml water supply per day till 21st day.
|
| Growth protocol |
Germinated seeds were sown in 4" pots containing vermiculite-perlite mixture and grown in net-house with ammonium nitrate as the only N source and other nutrients as per Yoshida media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from respective tissues using RNeasy Plant Mini Kit (Qiagen, Qiagen India Pvt. Ltd., New Delhi, India). RNA quality assessment was performed by using a RNA 6000 Nano assay kit in Bio analyzer 2100 (Agilent, Santa Clara, CA, USA). Samples with RIN value more than 7 were subjected to RNA-seq libraray construction using Illumina kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Shoot tissues of 15 day old plants were collected from IR 64 genotype from three independent biological replications
IAS
|
| Data processing |
Base calling done by illumina casava software
The raw data were processed by using the sickle tool for removing adaptors and low-quality reads. The Default parameters were considered for trimming the raw reads
CLC Genomics Workbench 12 used for transcriptome data analysis
Genome_build: IRGSP 1.0
Supplementary_files_format_and_content: Excel files includes TPM,RPKM values and etc for each sample.
|
| |
|
| Submission date |
Mar 18, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Amitha Mithra Sevanthi |
| E-mail(s) |
amithamithra.nrcpb@gmail.com
|
| Organization name |
ICAR - National Institute for Plant Biotechnology
|
| Street address |
LBS Centre, Pusa Campus
|
| City |
New Delhi |
| ZIP/Postal code |
110012 |
| Country |
India |
| |
|
| Platform ID |
GPL25149 |
| Series (1) |
| GSE147158 |
Genome-wide transcriptome changes under nitrogen (N), water (W) and N+W stress in root and shoot tissues of contrasting rice genotypes, IR 64 and Nagina 22 at seedling stage |
|
| Relations |
| BioSample |
SAMN14396856 |
| SRA |
SRX7945710 |
