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Introduction

This repository contains work done from an independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog on Zebrafish embryos using data from theSequence Read Archive (SRA).

The 3 main questions I'm trying to answer:

- Is binding strength of Nanog different between promoter and enhancer peaks?- Are there different sequence motifs found in promoter peaks vs enhancer peaks?- Is binding strength and binding sequence motif of your transcription factor at enhancerscorrelated with H3K27Ac histone modification levels?

Files

📜Supplementary Documentation.docx

Contains the specific commands used to perform ChIP-Seq analysis. This independent project utilizes High-Performance Computing cluster provided by University of PittsburghCenter for Research Computing (CRC).

📜nanog_heatmap.png

Preliminary results of comparing Nanog binding strength at promoters and enhancers. More work needs to be done in terms of analysis for the final publication written on this analysis.

Contact Information

Yogindra Raghav (YogiOnBioinformatics)

yraghav97@gmail.com