Table 2.
Multi-omics datasets for cell differentiation.
| Species | Cell line | Sequencing method | Data ID | Reference |
|---|---|---|---|---|
| Homo sapiens | Embryonic stem cell | Hi-C, RNA-seq, Chip-seq | GSE116862 | [41] |
| Hi-C, RNA-seq | GSE105028 | [42] | ||
| Hi-C, RNA-seq | GSE86821 | [43] | ||
| ChIP-seq, Dnase-HiC | GSE90680 | [44] | ||
| Hi-C, HiChIP, ChIP-seq, ATAC-seq, eU-Seq | GSE105028 | [42] | ||
| Hi-C,RNA-seq and ATAC-seq | GSE106687 | [45] | ||
| Hi-C | GSE107148 | |||
| Hi-C | GSE86821 | [43] | ||
| Hi-C | GSE52457 | |||
| Mus musculus | mESC | Capture Hi-C | GSE124698 | [46] |
| ATAC-seq, Hi-C,RNA-seq, ChIP-seq | GSE115933 | [47] | ||
| RNA-seq, ChIP-seq, Hi-C and Promoter Capture Hi-C | GSE100835 | [48] | ||
| Hi-C, RNA-seq | GSE89520 | |||
| ChIP-seq,Hi-C | GSE95533 | [49] | ||
| ChIP-seq,RNA-seq, ATAC-seq, WGBS and Hi-C | GSE138102 | [50] | ||
| Hi-C | GSE153884 | |||
| ChIP-seq,Hi-C and 5C | GSE156868 | [51] | ||
| In situ Hi-C | GSE118911 | [52] | ||
| ChIP-seq,ATAC-seq,Hi-ChIP,Hi-C | GSE113339 | |||
| RNA-seq,ChIP-seq, Xist CHART-seq, and in situ Hi-C | GSE116413 | [53] | ||
| Hi-C | GSE119805 | [54] | ||
| HiC,STEM-seq and RNA-seq | GSE109344 | [55] | ||
| ChIP-seq,RNA-seq, Hi-C | GSE119697 | [56] | ||
| Capture Hi-C | GSE114619 | [46] | ||
| Chip-Seq,Gro-Seq,Mnase-Seq, ATAC-seq and Hi-C | GSE82144 | [57], [58] | ||
| Hi-C | GSE110061 | |||
| Hi-C | GSE125656 | [59] | ||
| Hi-C | GSE146001 | [60] | ||
| Hi-C, RNA-seq | GSE118263 | [61] | ||
| Hi-C | GSE133246 | [62] | ||
| Hi-C | GSM4386021 | |||
| PLAC-seq. Hi-C, mRNA-seq and ChIP-seq | GSE146449 | [63] | ||
| Hi-C | GSE119347 | |||
| Hi-C | GSE124342 | [64] | ||
| Hi-C | GSE59027 | [65] | ||
| Hi-C, ChIP-Seq, RNA-Seq, DNase-Hypersensitivity | GSE72164 | [66] | ||
| DNA SPRITE, RNA-DNA SPRITE | GSE114242 | [67] | ||
| Hi-C | GSE130723 | |||
| Hi-C | GSE130725 | [68] | ||
| Hi-C, RNA-seq | GSE136307 | |||
| Hi-C | GSE152918 | [69] |
aEach column denotes the key properties of multi-omics data analysis of cell differentiation using Hi-C technology. ‘Species’ denotes the species’ name, ‘cell line’ column denotes the cell line that was analyzed, ‘sequencing method’ column denotes the sequencing methods that were used, ‘data ID’ column denotes the availability of the sequencing data, data ID GSEXXX can be searched in the NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi), ‘reference’ column denotes the references where the data were published. Readers are encouraged to seek out these papers for further information.