Hi-C Library Construction Protocol

Fresh leaves were cut into 2-cm pieces and fixed with 2% formaldehyde. Hi-C library construction was performed as previously described^{23 (link)}. In brief, genomic DNA was extracted, and the fixed chromatin was digested by DpnII, followed by a fill-in reaction with biotinylated nucleotides and proximity ligation. The DNA was purified and then sheared into ~ 350-bp fragments using a Covaris S220 device. The DNA fragments were subjected to blunt-end repair, A-tailing, Illumina paired-end adapter ligation and PCR amplification. The Hi-C library was sequenced on an Illumina NovaSeq PE150 instrument.

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Lv H., Wang Y., Han F., Ji J., Fang Z., Zhuang M., Li Z., Zhang Y, & Yang L. (2020). A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics. Scientific Reports, 10, 12394.

Publication 2020

S220 device paired-end adapter ligation NovaSeq PE150 instrument

Chromatin Device Formaldehyde Genomic Library Ligation Nucleotides

Corresponding Organization :

Other organizations : Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences

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Variable analysis

independent variables

Cutting fresh leaves into 2-cm pieces
Fixing the leaves with 2% formaldehyde

dependent variables

Hi-C library construction
DNA extraction
Chromatin digestion by DpnII
Fill-in reaction with biotinylated nucleotides
Proximity ligation
DNA purification
DNA shearing into ~350-bp fragments
Blunt-end repair
A-tailing
Illumina paired-end adapter ligation
PCR amplification
Hi-C library sequencing on Illumina NovaSeq PE150 instrument

control variables

Previously described Hi-C library construction method^{23 (link)}

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