GSM5133493: yZSJ025-HiC-rep2; Saccharomyces cerevisiae; Hi-C
ATAC-seq: 1,000,000 yeast cells were washed with 1mL RSB buffer (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) once and incubated for 60 min at 37 ℃ using zymolyase to digest cell walls (0.015 g/mL, Solarbio). Then the cell was resuspended in 1 mL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40, 0.1% Digitonin, 0.1% Tween-20, 1xProtease inhibitor) for 10 min at 4°C to lyse the yeast cell membrane to obtain the nucleus. Hi-C: Hi-C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocol(Rao et al., 2014). The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 150 bp high-throughput sequencing using illumina Nova-seq PE150 platform. ATAC-seq: Immediately following the nuclei prep, the pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was carried out for 30 min at 37 °C. Tn5 transposed DNA were purified by AMPure DNA magnetic beads. A qPCR reaction was performed on a subset of the DNA to determine the optimum number of PCR cycles. The amplified libraries were run on an Agilent Tapestation 2100 (Agilent Technologies) to detect size distribution of library fragments. Biological replicates were performed in duplicate for all ATAC experiments. Hi-C: Restriction fragment ends were labeled with biotinylated cytosine nucleotides by biotin-14-dCTP (TriLINK) followed by ligation. Purified DNA was sheared to a length of ~400 bp. Point ligation junctions were pulled down with Dynabeads MyOne Streptavidin C1 (Thermofisher). The Hi-C library for Illumina sequencing was prepped by NEBNext Ultra II DNA library Prep Kit for Illumina (NEB) according to the manufacturers' instructions. Fragments between 400 and 600 bp were paired-end sequenced on an illumina Nova-seq PE150 platform.