Table 1 Summary of single-cell Hi-C data for benchmark analysis
From: Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D
Data source | Cell type | # of cell | Interaction frequency | Off–diagonal interaction frequency | # of locus pairs | # of off–diag locus pairs | Mean off–diagonal interaction frequency per cell | Mean # of off–diagonal locus pairs per cell |
|---|---|---|---|---|---|---|---|---|
Ramani2017 [8] | GM12878, HAP1, Hela, K562 | 2610 | 51,420,688 | 23,089,064 (44.9%) | 16,639,155 | 11,081,243 (66.6%) | 8846.38 | 4245.69 |
Lee2019 [10] | Astro, Endo, L2/3, L4, L5, L6, MG, MP, Ndnf, ODC, OPC, Pvalb, Sst, Vip | 4238 | 4,586,887,008 | 553,896,738 (12.08%) | 132,310,725 | 120,126,414 (90.79%) | 130,821.2 | 28,371.85 |
Li2019 [9] | 2i, Serum1, Serum2 | 150 | 15,846,298 | 2,612,886 (16.49%) | 1,906,405 | 1,523,307 (79.9%) | 17,419.24 | 10,155.38 |
Kim2020 [15] | GM12878, H1Esc, HAP1, HFF, IMR90 | 9230 | 95,764,991 | 39,702,592 (41.46%) | 48,866,268 | 30,333,591 (62.07%) | 4305.2 | 3289.26 |