For ATAC-seq samples, 50,000 cells were lysed to obtain nuclei in cold lysis buffer, and incubated in the Tn5 transposase reaction mix, as described previously (Buenrostro et al., 2013). For ChIP-seq and input samples, cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Then, protein-DNA complexes were purified with anti-RARα antibody. For ATAC-seq samples, DNA fragments were PCR-amplified using previously-designed barcoded primers, as described previously (Buenrostro et al., 2013). For ChIP-seq and input samples, libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer's instruction.