Kanazawa et al., 2021
Cell Shape-Based Chemical Screening Reveals an Epigenetic Network Mediated by Focal Adhesions

Introduction

This repository contains the source code for the sequence analysis used in the above paper.

Chromatin immunoprecipitation-sequencing (ChIP-seq)

• ChIP_mapping.sh

RNA-sequencing (RNA-seq) analysis

• RNA_mapping.sh

Quantification and normalization of RNA-seq data

• featureCounts.sh
• Calculate_scaled_TPM_of_RNA-seq.R
• Rank_SE_associated_genes_by_expression_levels.R

Genomic alignment of ATAC-seq data

• ATAC_mapping.sh

Identification of super-enhancers (SEs), Gene assignment to SEs

• findPeaks_annotatePeaks.sh

Motif enrichment analysis

• Motif_enrichment_analysis.sh

Gene Ontology (GO) enrichment analysis

• GO_analysis_of_SE_associated_genes.R

Author

Hiroki Michida

License

MIT