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Table 1 Comparison of several sequencing methods

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