Table 1 Published datasets regarding chromatin regulation during regeneration

Axolotl

ATAC-seq

PRJNA682840

24 samples were collected including eight stages of axolotl limb regeneration: homeostatic, trauma (3 hpa), wounding healing (1 dpa), early-bud blastema (3 dpa), midbud blastema (7 dpa), late-bud blastema (14 dpa), palette stage (22 dpa) and re-differentiated stages (33 dpa) (Wei et al. 2021).

Hofstenia miamia

ATAC-seq

PRJNA515075

Hofstenia was amputated transversely and the regenerated tissues at different time points (at 0, 3, 6, 12, 24 and 48 hpa) were harvested (Gehrke et al. 2019).

Mouse

ChIP-seq

GSE104284

The injured and uninjured mice skeletal muscle at nine time points (3 h, 10 h, 24 h, 48 h, 72 h, 168 h, 336 h, 504 h, 672 h) were collected for H3K4me3, H3K4me1, and H3K27ac ChIP-seq (Aguilar et al. 2016).

GSE61316

Cultured or FACS-sorted mice hair follicle stem cells were collected for H3K27ac, H3K4me1, Crsp1/Trap220, and H3K27me3 ChIP-seq (Adam et al. 2015).

GSE71134

Percoll density gradient (37% versus 70%) was utilized to isolated microglial from injured and sham control spinal cord at 7 days post injury. These microglial were used for H3K4me1 ChIP-seq (Denk et al. 2016).

ATAC-seq

GSE135406

20 ATAC-seq libraries were generated for sorted Müller glia from retina at multiple time points following two retinal injury models (NMDA treatment for inner retinal injury and light damage for outer retinal injury) (Hoang et al. 2020).

GSE89928

The wound induced stem cells were sorted from Sox9^CreER;R26YFP mice with FACS and utilized to establish ATAC-sequencing library (Ge et al. 2017).

GSE92967

After 6 days, 30 days, and 180 days of IMQ treatment, the epithelial stem cells were purified from treated skin with FACS and utilized for ATAC-seq (Naik et al. 2017).

GSE158865

Mouse liver bulk ATAC-seq data was generated by harvesting hepatocytes nuclei of undamaged (0 h) and regenerating livers at 48 h, 72 h, and 96 h after PHx (Chen et al. 2020b).

scATAC-seq

GSE158873

Mouse liver scATAC-seq was performed on freshly isolated hepatocyte nuclei at 0, 48, 72, 96 h after PHx (Chen et al. 2020b).

GSE153479

Ventricles were collected after injury (myocardial infarction through surgery) at 3 day on P1 and P8 murine hearts for scATAC-seq (Wang et al. 2020d).

Rat

ChIP-seq

GSE63103

The sham control and injured rat P25 sciatic nerve samples were collected after 72 h post injury in rats for H3K27ac ChIP-seq (Hung et al. 2015).

Zebrafish

ATAC-seq

GSE135406

20 ATAC-seq libraries were produced for sorted Müller glia from retina at multiple time points following two retinal injury models (NMDA treatment for inner retinal injury and light damage for outer retinal injury) (Hoang et al. 2020).

GSE146960

Zebrafish whole-fin ATAC-seq libraries at 0 dpa (freshly amputated), 1 dpa and 4 dpa were generated (Thompson et al. 2020).

ChIP-seq

PRJNA559885

Zebrafish caudal fins were collected from amputation sites at 0 dpa and 1 dpa for H3K27ac and H3K4me3 ChIP-seq (Wang et al. 2020c).

GSE158104

Zebrafish regenerative cardiac tissues at 0, 6, 9 dpa were collected for H3K9ac and H3K9me3 ChIP-seq (Wang et al. 2022).

Xenopus laevis

ATAC-seq

ChIP-seq

PRJDB9147,

PRJDB13124

Proximal and intermediate Pax8:GFP positive nephric tubule cells were collected at day 0 (homeostatic), day 2 (regenerating), and day 5 (regenerated) for ATAC-seq and H3K27ac ChIP-seq (Suzuki et al. 2022).

African killifish

ChIP-seq

PRJNA559885

African killifish caudal fins were collected from amputation sites at 0 dpa and 1 dpa for H3K27ac and H3K4me3 ChIP-seq (Wang et al. 2020c).

Hydra

ATAC-seq

GSE127277

ATAC-seq was generated at different time courses including 0, 2, 4, 6, 12, 24 and 48 h during hydra head regeneration after head dissection (Murad et al. 2021).

ChIP-seq

GSE127278

H3K4me2, H3K4me3 and H3K27ac ChIP-seq were generated at different time courses including 0, 4, 6, and 24 h during hydra head regeneration after head dissection (Murad et al. 2021).

Drosophila

ATAC-seq

ChIP-seq

GSE102841

H3K4me1, H3K27ac, Pol II-8WG16, H3K27me3, Pol II phospho ser5 ChIP-seq were generated with early control and regeneration wing discs samples. For ATAC-seq, regeneration and control samples in different time points (early, mid, and late) were collected to establish ATAC-seq libraries (Vizcaya-Molina et al. 2018).