RNA-Seq and its Limitations:

• RNA sequencing (RNA-seq) enabled unbiased, high-throughput measurement of gene expression.
• It has revolutionized transcriptomics, helping in studies on differentiation, disease, and functional genomics.
• Limitation: RNA-seq does not reveal upstream chromatin and regulatory dynamics.

Chromatin Accessibility and ATAC-seq:

ATAC-seq uses Tn5 transposase (jumps to open chromatin → It inserts sequencing adapters into those open regions → adapters allow us to amplify and sequence only the open parts of the genome)

In short: An ATAC-signal shows how accessible a region of the genome is, based on how much Tn5 could cut and how many sequencing reads mapped there.

• Requires fewer cells.
• Simpler and faster protocol.
• High-resolution insights into chromatin structure.
• Allows inference of nucleosome positioning and TF binding

Main idea: Joint analysis of chromatin accessibility and gene expression reconstructs regulatory networks that define cell states and transitions.

In simpler terms:

We are using a method called ATAC-seq to find open regions of the DNA, where important genes can be turned on or off. Our goal is to link these open regions — called regulatory elements — to the genes they control, and to understand how different immune cells use different parts of their DNA to become specialized.