Cell-type specific chromatin landscape in the human brain

FIRE folder: code used for FIREs analyses

1. Identification of FIREs in NeuN+ and NeuN- cells
2. Definition of differential FIREs between NeuN+ and NeuN- FIREs cells
3. Overlap differential FIREs with differential H3K27ac ChIP-seq in NeuN+ and NeuN- cells
4. Cellular expression levels of genes assigned to differential FIREs in NeuN+ and NeuN- cells

superFIRE folder: code used for super-FIREs analyses

1. Identification of super-FIREs in NeuN+ and NeuN- cells.
2. Overlap super-FIREs with differential H3K27ac ChIP-seq in NeuN+ and NeuN- cells
3. Cellular expression levels of genes assigned to super-FIREs in NeuN+ and NeuN- cells

NeuN_Loops folder: code used for enhancer-promoter interactions analyses

1. Comparison between TADs and promoter-anchored interactions
2. Cellular expression levels of genes assigned to enhancer-promoter interactions in NeuN+ and NeuN- cells
3. TF motif analysis and expression levels of corresponding TFs

Glu_GABA folder: code for Glu and GABA loop analysis

1. Linking Glu vs. GABA H3K27ac peaks to their cognate genes using NeuN+ promoter-anchored interactions
2. Cell-type specific expression levels of genes assigned to Glu vs. GABA enhancer-promoter interactions