Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing ...

(陈玲玲老师团队的ceRNA分析)

Introduction

Inorganic phosphate (Pi) is essential for the growth and productivity of plants;
The competing endogenous RNA (ceRNA) theory has been proved and is now acknowledged widely;
lincRNAs compete with genes to play important roles in rice undergoing Pi starvation.

Methods

RNA-seq data
数据质控:quality control (QC) toolkit
比对到参考基因组:tophat tool
合并重复:Samtools
组装:Cufflinks
最终组装:Cuffmerge
间隔区的选择:Cuffcompare
蛋白编码能力预测:Coding Potential Assessment Tool (CPAT) 和Coding Potential Calculator


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