Nextseq 2k

Total RNA was extracted from mice eye ball (n = 3) using RNeasy mini kits (Qiagen) following the manufacture's instructions followed by DNase treatment. The concentration of RNA was checked using the NanoDrop Spectrophotometer (Biorad), NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and Qubit 4 Fluorometer (Thermo Fisher Scientific, Indianapolis, IN, USA), whereas RNA quality was assessed with the Tapestation 4200 (Agilent Technologies, Santa Clara, CA, USA).
The cDNA was synthesized using reverse transcriptase and random hexamers in a first strand synthesis reaction. Prepared libraries were sequenced on Illumina Nextseq 2K to generate 40 M, 2 × 150 bp reads /sample. Up to 75% of the sequenced bases were of Q30 value > 90. Sequenced data were processed to generate FASTQ files and proceeded with data analysis.

Cells were cross-linked with 1% formaldehyde and quenched in 125 mM glycine. Chromatin was isolated using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology), sonicated to 200 to 300 bp in length, and subjected to IP with ZMYND8 (Bethyl Laboratories) or H3K14ac (Abcam) antibody (table S2). ChIP DNA libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina and sequenced on the Illumina NextSeq 2 K. Bioinformatics were performed as described previously (12 (link)).