this transcriptome shotgun assembly project has been deposited at ddbj / embl / genbank under the accession gdkm00000000 .
high yielding rice cultivars need high quantities of nitrogen which is usually supplied in the form of urea fertilizers .
rice cultivars show diversity in their nitrogen use efficiency which influences the yield of particular cultivars .
nitrogen use efficiency is influenced by nitrogen uptake , transport , vacuolar storage , utilization and remobilization .
so , it is necessary to understand the molecular basis of nitrogen use efficiency of high yielding rice cultivars for understanding the basis of their high yield .
the high throughput rna - seq analysis enables understanding of the functioning of all genes at a particular time and location . in this work rna - seq analysis
is employed for understanding the genomic basis behind nitrogen use efficiency of the high yielding indica rice cultivar rpbio-226 .
rp bio-226 seeds were surface sterilized with 0.1% hgcl2 for 30  min , rinsed thoroughly with distilled water and germinated on murashige and skoog medium that lacked a nitrogen source .
ten day old seedlings were transferred to 0.1  mm urea containing murashige and skoog medium .
total rna was isolated from the leaves and rna concentration and purity were estimated with a nanodrop spectrophotometer .
mrna was purified and fragmented at elevated temperature ( 94  c ) in the presence of divalent cations .
first strand cdna synthesis was carried out by fragmented mrna and reverse transcribed with superscript iii reverse transcriptase by using random hexamers .
illumina adapters were ligated to the cdna molecules after end repair and addition of  a base .
the library was amplified using 8  cycles of pcr for enrichment of adapter ligated fragments .
the prepared library was quantified using qubit and validated for quality by running an aliquot on high sensitivity bioanalyzer chip .
the effective sequencing insert size is 130580 ; the inserts are flanked by adapters whose combined size is 120  bp .
transcriptome sequencing was carried out with the illumina_nextseq500 system ( illumina , san diego , ca ) .
the preprocessing of the reads was performed with fastqc and the adapters were removed with fastx toolkit , .
samtools ( ver 0.1.18 ) and snpeff ( ver 4.1 ) were used for creation of variation report with a mapping quality of >  30 and read depth of >  20 as cutoffs , .
de novo transcriptome assembly was performed with velvet and oases softwares ,   ( table 1 ) .
we have planned to analyze the transcriptome of rp bio 226 in comparison with other rice cultivars for understanding the variation in nitrogen use efficiency of rice .
 rice yield is greatly influenced by the nitrogen and rice varieties show variation in yield . for understanding the role of urea nutrition in the yield of elite indica rice cultivar rpbio-226 , 
 the urea responsive transcriptome was sequenced and analyzed . the raw reads and 
 the transcriptome shotgun assembly project has been deposited at ddbj / embl / genbank under the accession gdkm00000000 . 
 the version described in this paper is the first version , gdkm01000000 . 
Direct link to deposited data
Experimental design, materials and methods