From: Detect accessible chromatin using ATAC-sequencing, from principle to applications
Methods | MNase-seq | DNase-seq | FAIRE-seq | ATAC-seq |
---|---|---|---|---|
Cell status | Any state of cells | Any state of cells | Any state of cells | Fresh cells or slowly cooled cryopreserved cells |
Principle | MNase digests DNA which is not protected by protein or nucleosome on chromatin. | DNAase I preferentially excises DNA sequence without nucleosomes. | Separation of naked DNA based on formaldehyde fixation and phenol-chloroform extraction | Tn5 transpoase inserts the DNA sequence without protein or nucleosome protection and excises it. |
Target regions | Focus on nucleosome localization | Accessible chromatin regions, focusing on transcription factor binding sites | Accessible chromatin regions | Accessible chromatin regions in genome-wide, including transcription factors, histone modifications. |
Specific features | 1. A large number of cells as input materials; 2. The quantity of enzyme needs to be accurate; 3. Localization of the entire nucleosome and inactive regulatory region; 4. Detecting inactive regions by degrading active regions; 5. Standard analysis requires 150-200 M reads. | 1. A large number of cells as input materials; 2. The process of sample preparation is complicated; 3. The quantity of enzyme needs to be accurate; 4. Standard analysis requires 20-50 M reads. | 1. Low signal-to-noise ratio makes data analysis difficult; 2. Results depend heavily on formaldehyde fixation; 3. Standard analysis requires 20-50 M reads. | 1. A lower number of cells as input materials; 2. Standard analysis requires 20-50 M reads through reducing sequencing depth; 3. Conveniently obtain accessible chromatin regions in genome-wide; 4. Mitochondrial data has an effect on the accuracy of the results. |
Time | 2–3 days | 2–3 days | 3–4 days | 2–3 h |