What is ATAC-seq footprinting?

a The concept of footprinting using ATAC-seq. Tn5 transposase cleaves DNA and inserts sequencing adapters, but is unable to cut chromatin occupied by proteins such as nucleosomes (gray) and other DNA binding proteins e.g., transcription factors (blue).

What does ATAC-seq measure?

The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) is a popular method for determining chromatin accessibility across the genome. By sequencing regions of open chromatin, ATAC-Seq can help you uncover how chromatin packaging and other factors affect gene expression.

What is SCI ATAC-seq?

ATAC-Seq is an assay for interrogating the entire genome for accessibility to DNA binding proteins in a single experiment. The technique scales sublinearly in time and cost and can profile thousands of individual cells in a single experiment.

What is the difference between ATAC-seq and ChIP-seq?

The genome-wide chromatin accessibility profile detected using ATAC-seq represents another level of the chromatin regulatory landscape compared to ChIP-seq, which directly determines specific DNA-protein interactions (Table 2).

How is hint used in ATAC seq analysis?

Finally, we use HINT to generate average ATAC-seq profiles around binding sites of particular TF. This analysis allows us to inspect the chromatin accessibility for each particular TF. Moreover, by comparing the cleavage profiles from different ATAC-seq libraries, we can get insights on changes in binding in two cells.

How does differential footprints on single cell ATAC Seq work?

This analysis allows us to inspect the chromatin accessibility for each particular TF. Moreover, by comparing the cleavage profiles from different ATAC-seq libraries, we can get insights on changes in binding in two cells. For this, execute the following commands:

How to create a single cell ATAC-seq library?

To characterize the transcription factors that control these tow sub-clusters, we merged the cells from each of the sub-clusters and created a cluster-specific ATAC-seq library, named as MEP1 and MEP2 . The other cells were collected as Others. 1. Download the data here and extract the pre-processed data with the following commands:

What are the types of peak callers for ATAC-seq?

Popular peak callers for ATAC-seq can be divided into two major categories: count-based or shaped-based. The count-based peak callers employ different statistical methods to compare read distribution shape in a candidate region to a random background.