Computational protocol: Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis

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Protocol publication

[…] Reads were mapped onto the Arabidopsis genome (TAIR10) using Bowtie (v0.12.9) without allowing mismatches (). Mapped reads were counted using the Bedtools (v2.17.0) script coverageBed () with the annotation file from miRBase (http://www.mirbase.org/). For mature miRNAs we counted only reads that matched perfectly to the miRBase annotated region without any shift. The differential expression analysis was performed with Bioconductor (2.13) package DESeq (). MiRNAs were declared as differentially expressed if the adjusted P-value (padj) was below 0.1. To determine miRNAs differentially expressed in the tough mutant () the read counts of the dataset (GSE38600) were used. […]

Pipeline specifications

Software tools Bowtie, BEDTools, DESeq
Databases TAIR miRBase
Application sRNA-seq analysis
Organisms Arabidopsis thaliana