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Sample GSM4419429 Query DataSets for GSM4419429
Status Public on Dec 15, 2020
Title IR64_N-W+_root
Sample type SRA
 
Source name Root
Organism Oryza sativa
Characteristics cultivar: IR 64
tissue: Root
growth stage: Seedling
stress: Nitrogen 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 Root tissues of 15 day old plants grown under chronic nitrogen stress (0.04 mM NH4NO3) were collected from IR 64 genotype from three independent biological replications.
IBR
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 SAMN14396855
SRA SRX7945711

Supplementary file Size Download File type/resource
GSM4419429_IBR.xlsx 5.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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