A study of Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization. Sijie Zhou et al.
Description
The sequencing of SCRaMbLEd populations. SCRaMbLE of the strain yZSJ025 to generate a SCRaMbLEd pool(yZSJ400). yZSJ400 has a different sequencing depth from yZSJ490
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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.