BMP9_FSS_ATAC_analysis

Scripts used in the data analysis of the paper titled as BMP9 and Fluid Shear Stress regulate endothelial chromatin accessibility and expression of SMAD low affinity target genes

The paper analyses ATAC-seq data of 4 different conditions:

conditions	with BMP	witho BMP
with FSS	1. BMP9_flow	2. control_flow
witho FSS	3. BMP9_static	4. control_static

Analysis steps: 0. Pre-process the data according to ENCODE ATAC-seq pipeline

1. Which regions are common and differentially accessible in different conditions | Find differentially accessible regions

• Differential accessibility analysis via DiffBind || vignette

2. What are the closest genes to the differential regions | Annotate the differential regions by the closest promoter in gene symbol || vignette

3. What is the overlap of the accessible regions between different conditions || vignette

4. Which TFs are enriched in the interested regions of interests || vignette

   Find enriched motif sequences within the differentially accessible regions for:

   a. Regions specific to BMP9 stimulation only: BMP9_static VS control_static

   b. Regions specific to flow only: control_flow VS control_static

   c. Regions different between BMP9 stimulation and flow: (BMP9_static VS control_static) VS (control_flow VS control_static)

• Reformat the input for HOMER
• Perform de novo and known motif enrichment analysis via HOMER

4. We are interested in 3 TFs (GC-SBEs, 5bp GC-SBEs and SBEs) found in the analysis. What are the Further investigate the 3 TFs: GC-SBEs, 5bp GC-SBEs and SBEs

• Find the BMP9 specific regions that can be bound by the above-mentioned TFs & Obtain the sequences of these regions || [vignette]vignettes/get_regions_binging_both_motif5_and_motif6_200bp.ipynb)
• Find the number of sequence matches for each TF || vignette