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.
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.