Michida et al., 2020
The number of transcription factors at an enhancer determines switch-like gene expression

Introduction

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

Relative paths under “src” are shown.

ATAC sequencing and genomic alignment

Primary_analysis/ATAC-seq_mapping.sh

ChIP sequencing and genomic alignment

Primary_analysis/ChIP-seq_mapping.sh

Single cell RNA sequencing and genomic alignment

Primary_analysis/scRNA-seq_mapping.sh
Primary_analysis/featureCounts.sh
Fig2/SCDE.R

Identification of SEs and TEs

Primary_analysis/Call_SE_TE.sh
Fig1/Fig1A.R
Fig1/Get_venn_num.sh
Fig1/Fig1B.R
Primary_analysis/Make_enhancer_catalog.sh
Fig1/Fig1D.R

ATAC-seq coverage in SEs and TEs

Sup_figs/SFig1D.sh
Sup_figs/SFig1D.R

Quantification of ChIP and ATAC signals in enhancer and proximal TSS regions

Primary_analysis/Make_bigwig.sh
Primary_analysis/multiBigwigSummary.sh
Fig1/Fig1C_E-H.R

Gene assignment to enhancers

Fig2/Gene_assignment.R

Identification of RelA binding numbers from sequence data

Primary_analysis/Peak_call_for_bulk.sh
Fig3/Extend_bulk_ATAC_peaks.R
Fig3/Get_RelA_peaks_in_ATAC_peaks.sh
Fig3/RelA_peak_motif_count.R

Motif analysis

Fig4/Fig4A-D.sh
Fig4/Fig4E.R

Identification of NF-κB and PU.1 motifs

Fig4/Peak_call_for_scATAC.sh
Fig4/Extend_sc-ATAC_peaks.R
Fig4/intersectBed_get_PU1_position_for_scATAC.sh
Fig4/Count_RelA_PU1_overlap_for_scATAC.sh
Fig4/Fig4E.R
Fig5/Get_PU1_motifs_in_enhancers.sh
Fig5/Get_RelA_PU1_overlap.sh
Fig3/Get_NFkB_motifs_in_enhancers.sh
Fig3/RelA_peak_motif_count.R
Sup_figs/SFig6A.R

Gene Ontology (GO) analysis

Sup_figs/SFig1A.R

Mathematical modeling

Fig3/Filtering_genes.R
Fig3/Fig3B_D.R
Fig3/Fig3F.py
Sup_figs/SFig4D.R
Fig5/Fig5A-E.R

Prediction of single cell mRNA distribution using a mathematical model

Fig3/Parameter_estimation.py

Authors

Hiroki Michida and Hiroaki Imoto

License