TABLE 5.
Chromatin accessibility datasets used for annotating heart enhancers.
| Methods | Species | Samples | Condition | Stage | References |
| ATAC-seq | Ciona | B7.5 lineage | WT | 6 hpf (native mesoderm),18 hpf (committed heart and pharyngeal muscle precursors) | Racioppi et al., 2019 |
| ATAC-seq | Ciona | B7.5 lineage | WT, Fgfr dominant-negative, Mek constitutively active, Foxf-CRISPR, M-Ras constitutively active | 10 hpf (multipotent cardiopharyngeal progenitors) | |
| ATAC-seq | Zebrafish | myl7:GFP+ cardiomyocytes | WT, gata5 -/-, hand2 -/-, tbx5 -/- mutants | 72 hpf | Pawlak et al., 2019 |
| ATAC-seq | Mouse | Heart | WT | E12.5 | Zhou et al., 2017 |
| ATAC-seq | Mouse | Heart | WT | P1, P14, P56 | Quaife-Ryan et al., 2017 |
| ATAC-seq | Mouse | endocardial cells | WT and TBX20 KO | E12.5 | Boogerd et al., 2017 |
| ATAC-seq | Mouse | Nkx2-5+ cardiac progenitor cells | WT | E7.5, E8.5, E9.5 | Jia et al., 2018 |
| ATAC-seq | Mouse | Isl1+ cardiac progenitor cells | WT and Isl1 KO | E8.5, E9.5 | |
| ATAC-seq | Mouse | Isl1+/CD31+, Isl1+/CD31- cardiac progenitor cells | WT | E8.5, E9.5 | |
| ATAC-seq | Mouse | Isl1+ cardiac progenitor cells | Nkx2.5 overexpression in Isl1+ cells | E9.5, E12.5 | |
| Single-cell ATAC-seq | Mouse | Isl1+ cardiac progenitor cells | WT | E8.5, E9.5 | |
| Omni-ATAC-seq | Mouse | Heart | WT | Adult | Liu et al., 2019 |
| ATAC-seq | Mouse | Ventricle cardiomyocytes | WT | E12.5 | Akerberg et al., 2019 |
| ATAC-seq | Mouse | Cardiac pacemaker cells (PCs), right atrial cardiomyocytes (RACMs) | WT | Neonatal (P0-P2) | Galang et al., 2020 |
| Single-cell ATAC-seq | Mouse | Ventricle | myocardial infarction (MI) or sham surgeries | P1, P8 (3days post surgeries for both) | Wang et al., 2020 |
| ATAC-seq | Human | ESCs, ESC-differentiated cells | WT | ESCs, mid primitive streak, lateral mesoderm, cardiac mesoderm | Loh et al., 2016 |
| ATAC-seq | Human | iPSC-differentiated cells | WT, GATA4_G296S | iPS-derived cardiac progenitor cells | Ang et al., 2016 |
| ATAC-seq | Human | ESCs, ESC-differentiated cells, iPSCs, iPSC-differentiated cells | WT | ESCs and iPSCs, mesoderm, cardiac mesoderm, cardiomyocyte | Liu et al., 2017 |
| ATAC-seq | Human | ESCs, ESC-differentiated cells, iPSCs, iPSC-differentiated cells | Control and INN (isotretinoin) treatment | ESCs and iPSCs, mesoderm, cardiac mesoderm | Liu et al., 2018 |
| ATAC-seq | Human | ESCs, ESC-differentiated cells | WT | ESCs, mesoderm, cardiac progenitors, cardiomyocytes | Bertero et al., 2019 |
| ATAC-seq | Human | ESC-differentiated sinoatrial node-like pacemaker cells (SANLPC), ventricle-like cardiomyocytes (VLCM), | WT | ESC-differentiated cardiomyocytes | van Eif et al., 2020 |
Data from large consortiums (ENCODE, FANTOM, and Roadmap Epigenomics Projects) are not listed. Datasets are sorted by species first and then by publication dates.