Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 4
Release date: Dec 31 2016
Last update date: Dec 31 2016
Access: Public
Diseases: Disorders of Sex Development
Chemicals: Iron
Dataset link Differential gene expression in developing grains of two tropical indica rice genotypes differing in grain iron concentration through RNA-seq

Experimental Protocol


CRD was used to grow rice plants in the net house under ambient condition. Plants Sharbati and Lalat having contarsting grain Fe concentration (24.88 ppm and 7.80 ppm of Fe in the brown rice samples of Sharbati and Lalat, respectively) [Panda et. al., 2014] were grown in the net house. One week old seedlings were transferred to plastic pots filled soil and farm yard manure in 3:1 ratio and grown in the net house under ambient conditions till maturity. Fifteen days after panicle emergence (mid-grain-filling stage) roots and developing grains were collected, washed in sterile nanopure water, blotted, dipped in RNA stabilizer solution in a falcon tube and stored in refrigerator for 24h. The tubes were sifted to -80oC ultra freezer for until future use. Differences in gene expression between different samples were tested with Cuffdiff package of Cufflinks using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) from reference-guided mapping. Genes expressed at very low levels (read counts < 10 across all six libraries) were not used in analysis of differential gene expression. Significance tests for differential expression were based on a modified exact test. A false discovery rate (FDR) of 0.05 and p-value ≤0.05 was used for identifying differentially expressed genes.

Repositories


GEO

GSE70093

ENA

SRP059726

BioProject

PRJNA287628

Download


Contact


Avijit Das