Sharyn E Perry

Introduction:

We study the molecular mechanism in seed development in plants. We focus on gene regulatory networks in embryogenesis. Most importantly we have Transcription Factors (TF) regulating the embryogenesis and we are interested in elucidating the direct and indirect targets of those TFs. Our lab mainly does Chromatin Immunoprecipitation (ChIP) and gene expression analysis. We combine Next generation sequencing (ChIP- seq and RNA-seq) to study at genomic level for model plant Arabidopsis.

Project 1: Identify the genome wide binding

We will map the genome wide binding of the protein of our interest using ChIP and perform Illumina sequencing.

Computational method:

Read processing, quality checking, read mapping, annotation, and peak calling.

Software: 

Trinity , BLAST, MACS2, Bowtie, (R- Bio conductor).

Project 2: Gene expression analysis

We will use RNA-seq to profile global gene expression of mutant and control plants involved in embryogenesis.

Computational methods:

Read processing, transcriptome assembly, read mapping, annotation and differential expression analysis.

Software:

Trinity , BLAST, RSEM, DESeq2 (R- Bio conductor)

Students:

Sanjay Joshi, Graduate, Added 06/21/2021

Grants:

Publications: