HiC samples for mammalian cells were carried out using the Arima-HiC Kit (A510008, ARIMA Genomics) with some modifications. Briefly, the nuclei were prepared from 3 million cross-linked cells (−80°C) using Nuclei EZ prep (NUC101, Sigma-Aldrich) at 4°C for 10 min and spun down 500 × g at 1°C for 5 min. The nuclei wash was carried out in 0.09% bovine serum albumin (BSA)/CapC lysis buffer (10 mM Tris–Cl pH 8.0, 10 mM NaCl, 0.2% NP40, 0.09% BSA, and 1 tablet of EDTA-free protease inhibitor cocktail (11873580001, Roche) per 50 ml) at 4°C for 10 min and spun down at 500 × g at 1°C for 5 min. The nuclei pellets were resuspended in 25 μl of nuclease-free H2O (total volume of nuclei is ~30 μl). A 20-μl solution (~2 million) of freshly prepared nuclei was used for HiC sample preparation.
HiC libraries were generated using the Arima Library Prep module (A303011, ARIMA Genomics) as described by the manufacturers and sequenced using a NovaSeq6000 (Illumina). We used Illumina 150 bp paired end sequencing (300 cycle) to obtain ~1 billion read-pairs per sample.
The HiC dataset consists of the two biological replicated samples in OE19 cells. The paired-end reads of each sample were aligned to the human genome hg38 by the aligning software BWA-MEM v0.7.17 (Li and Durbin, 2010 (link)). The uniquely mapped reads were processed by the HiC data analysis pipeline Juicer v1.6 (Durand et al., 2016 (link)). The contacts identified in each of the two samples were stored in the.hic files. We applied the R package HiCRep with the default settings (Yang et al., 2017 (link)) to the contacts at MAPQ ≥ 30 to calculate the stratum-adjusted correlation coefficient (SCC) between the two replicates. As HiCRep calculated the SCC for the contacts on each chromosome, we calculated the chromosome-length weighted average of the SCCs on all the chromosomes as a summary SCC. The summary SCC for the two replicates is 0.965. We also applied the Juicer pipeline to the pool of the aligned reads from the two replicates and obtained the contacts from the merged reads of the two replicates.
The HiC data files of the two samples were uploaded in ArrayExpress repository with the ArrayExpress data ID E-MTAB-12664.
HiC libraries were generated using the Arima Library Prep module (A303011, ARIMA Genomics) as described by the manufacturers and sequenced using a NovaSeq6000 (Illumina). We used Illumina 150 bp paired end sequencing (300 cycle) to obtain ~1 billion read-pairs per sample.
The HiC dataset consists of the two biological replicated samples in OE19 cells. The paired-end reads of each sample were aligned to the human genome hg38 by the aligning software BWA-MEM v0.7.17 (Li and Durbin, 2010 (link)). The uniquely mapped reads were processed by the HiC data analysis pipeline Juicer v1.6 (Durand et al., 2016 (link)). The contacts identified in each of the two samples were stored in the.hic files. We applied the R package HiCRep with the default settings (Yang et al., 2017 (link)) to the contacts at MAPQ ≥ 30 to calculate the stratum-adjusted correlation coefficient (SCC) between the two replicates. As HiCRep calculated the SCC for the contacts on each chromosome, we calculated the chromosome-length weighted average of the SCCs on all the chromosomes as a summary SCC. The summary SCC for the two replicates is 0.965. We also applied the Juicer pipeline to the pool of the aligned reads from the two replicates and obtained the contacts from the merged reads of the two replicates.
The HiC data files of the two samples were uploaded in ArrayExpress repository with the ArrayExpress data ID E-MTAB-12664.
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