Name:Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress 

Link to publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798287/

NCBI bioproject ID: PRJNA304223

Category: RNA-Seq, stress

Description:
The seeds of maize inbred line B73 were surfaced-sterized in 0% (v/v) H2O2 for 40 min, rinsed five times by distilled water, and germinated at 28°C with a 14/10 h light/dark photoperiod.
The seedlings were removed from the endosperm after two leaves were visible and transferred into pots containing 2L of nutrient solution.Seedlings with uniform growth were picked randomly 
and divided into the normal nitrogen group (N-4mM, normal-N) and the low nitrogen group (N-0.04mM, low-N). The nitrogen source was obtained from Ca(NO3)2·4H2O and Ca2- deficiency was supplemented 
with CaCl2. The plants were then grown at 28/22°C with a 14/10 h light/dark cycle and 70% humidity treatment. The roots of maize plants were collected at 12 h, 24 h, 48 h and 96 h after two N treatments.


Total RNA was isolated from the roots of normal and lower nitrogen group for the various time points using Trizol reagent (Invitrogen,USA) following the manufacturer's instructions.
RNA-seq reads were mapped by MaizeGDB to Zm-B73-REFERENCE-NAM-5.0. using STAR. Bigwig files were generated using bedtools genomecov -split -scale 1.0 
followed by kentUtils bedGraphToBigWig.