GSM5769457: Untreated_DTR_Utricle_scATACseq; Danio rerio; ATAC-seq
For single-cell experiments, non-regenerating (untreated) and regenerating inner ears (saccule and utricle) were dissected at consecutive time-points and dissociated into single-cells using trypsin and collagenase. For bulk ATAC-seq experiments, untreated inner ears (saccule and utricle) were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA-seq, cDNA libraries were generatated with Chromium Controller and Chromium Single Cell 3' GEM, Library and Gel Bead Kit V3 (10x Genomics). For scATAC-seq, libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit (1000111, 10X Genomics). For bulk ATAC-seq, libraries were generated using Nextera DNA Library Preparation Kit (Catalog # FC-121-1030). Transposed DNA were amplified by PCR with indexed primers and libraries were purified.