Hi-C sequencing

Hi-C Sequencing Services: Chromosome Conformation Capture 

Hi-C is used to assign contigs to chromosomes and assist in de novo genome assembly. It is usually combined with PacBio Revio long read and Nanopore ultra-long read sequencing to create an optimal genome assembly. All three services are offered at the gCore.

Hi-C is a genomic technique that captures the three-dimensional structure of chromosomes, shedding light on how genomic regions interact within the cell nucleus. This method begins by cross-linking DNA, which preserves the spatial arrangement of chromatin. The DNA is then digested, the ends are filled in with biotinylated nucleotides, and the fragments are ligated together. Sequencing these ligation products reveals which DNA regions were physically close in the nucleus despite being distant in the linear genome sequence.

Hi-C data provides insights into chromosomal territories by illustrating how different regions of the genome cluster together spatially. 

Introductory UCSD price: 

• Sample should be submitted as frozen tissue. 

  • 50-200 mg of tissue is recommended for large animals when possible. Lower inputs may work on a case-by-case basis; contact tbiddle@health.ucsd.edu prior to submitting sample.

  • For best results, tissue should be flash-frozen immediately and stored at a minimum temperature of -75 C. 

• Library prep (reagents and labor): $1000 per sample

• Sequencing: $900 per sample (for 3 Gbps-long genomes)

  • Should be sequenced using on a PE150 (2 x 150 bp) flow cell. Sequencing depth should be approximately 200 M reads per 1 Gbp.

• Total:  $1900 per sample

• Contact Max at mrempel@ucsd.edu for the bioinformatics price estimate. 

• Contact Trevor at tbiddle@health.ucsd.edu for protocol details and sample submission