The Applied Bioinformatics Laboratories offer analysis of Hi-C sequencing, or Hi-C-seq, data. Chromatin conformation capture assays that are used to detect genome-wide DNA–DNA interactions.

Request a Hi-C-Seq Service

To request this service from us, please provide the following:

• a sample sheet with the corresponding conditions for the samples
• the organism(s) of the particular study
• the restrictions enzyme(s) using for Hi-C library preparation
• the link to the generated FASTQ data (obtained from NYU Langone’s Genome Technology Center or another sequencing facility)

You receive the following from us:

• a comprehensive report
• genome browser tracks for visualization with the WashU Epigenome Browser
• a principal component analysis plot for assessment of sample variations
• per-sample matrices with (normalized) interaction frequencies
• per-sample matrices with topologically associating domain (TAD) boundary strength scores
• per-sample lists of TAD calls
• matrix of chromatin DNA–DNA interactions annotated by gene

Additional or Customized Analyses

We also provide the following analyses:

• differential TAD activity analysis
• TAD disruption analysis
• integrative analyses with RNA-seq data
• integrative analyses with H3K27ac, CTCF, or other ChIP-seq data
• virtual 4C for selected loci

Each of these may be subject to an additional charge.

Additional Resources

Below is a link to a computational pipeline that we typically use for our analyses:

• Hi-C–bench platform (hicseq–standard pipeline)

The following select publications have used our analyses:

• Lazaris C, Kelly S, Ntziachristos P, Aifantis I, Tsirigos A. HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genomics. 2017;18(1):22.
• Gong Y, Lazaris C, Sakellaropoulos T, Lozano A, Kambadur P, Ntziachristos P, et al. Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries. Nature Communications. 2018;9(1):542.