title: HIC-Seq of Phthonandria atrilineata: adult mussle
design: Hi-C libraries for Phthonandria atrilineata were prepared using a modified in situ Hi-C protocol. Fresh adult specimens were dissected, and muscle tissue was crosslinked with 1% formaldehyde for 10 minutes at room temperature. The crosslinking reaction was quenched with 0.125 M glycine for 5 minutes. Crosslinked tissue was homogenized and lysed in Hi-C lysis buffer containing protease inhibitors. Chromatin was digested using the restriction enzyme HindIII (400 U) at 37C for 4 hours. Digested ends were filled in with biotin-14-dATP using Klenow enzyme, followed by proximity ligation at room temperature for 4 hours.After reversal of crosslinks, the DNA was purified and sheared to 300-500 bp fragments using a Covaris S220 ultrasonicator. Biotin-labeled fragments were enriched using streptavidin beads. The Hi-C library was then prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer's instructions. Library amplification was performed using NEBNext Multiplex Oligos for Illumina (New England Biolabs) with 8-10 PCR cycles. The final library was size-selected using AMPure XP beads to obtain an average insert size of 300-400 bp. Library quality and quantity were assessed using an Agilent 2100 Bioanalyzer and qPCR with the KAPA Library Quantification Kit (Kapa Biosystems). The Hi-C library was sequenced on an Illumina NovaSeq 6000 platform using 150 bp paired-end sequencing mode.
library_name: PHAT_HIC_2024
identifiers.namespace: SUB14765118
identifiers.id: PHAT_HIC_2024