Frequently Asked Questions

While a cell or tissue sample comprising 3ug of DNA is the recommended input amount for the Arima-HiC assay, it is possible to produce high quality Arima-HiC libraries from much fewer cells (e.g. ~100,000 human cells or less, depending on the application)

Arima-HiC chemistry is robust and works across a variety of genome compositions. If your genome of interest has unique properties, Arima can run an in silico analysis to inform Arima-HiC assay compatibility.

Each Arima Hi-C kit contains 8 reactions. One reaction is typically sufficient for the generation of ~600M raw read-pairs. More precise estimates of library complexity can be determined from the Arima-QC2 assay as outlined in our User Guide.

The Arima-HiC protocol is a fast, user-friendly workflow that takes on average 6 hours total time with 1 hour hands-on time. The Arima-HiC protocol is followed by library preparation to generate Arima-HiC libraries that are ready for Illumina sequencing.

Yes, the Arima-HiC kit can be used for Capture-HiC studies. For help with Capture-HiC probe design or more information on compatible capture hybridization protocols, please contact Technical Support.

Yes, the Arima-HiC kit can be used for HiChIP and PLAC-Seq studies.

Yes. Arima recommends crosslinking using 2% formaldehyde (see our User Guide for more details). Crosslinking with different strengths of formaldehyde (e.g. 1%) has also worked with comparable performance. However, we do not recommend using <1% formaldehyde.

Arima currently provides pre-validated custom library prep user guides for KAPA HyperPrep, Swift Accel-NGS 2S Plus, Agilent SureSelect XT, Illumina TruSeq, NEBNext Ultra II, and others. Please contact an Arima representative to inquire about a pre-validated user guide for your preferred library prep kit.

We strongly recommend following the Arima user guide and use 100ul for shearing. We have validated that shearing in 100ul of volume in Covaris microtubes produces comparable results to 130ul. Perhaps more importantly, the DNA Size Selection protocol following DNA shearing uses specific SPRI bead to sample volume ratios for bead-based size selection. If 130ul of volume is used as input to the size selection protocol instead of 100ul, the resulting DNA sizes will be considerably larger than expected and may negatively impact library prep and sequencing performance.

The preparation of Arima-HiC libraries requires a centrifuge for pre-HiC sample prep, a thermomixer or thermal cycler for heated incubations, a Covaris or Diaganode sonicator for DNA shearing, a thermal cycler for PCR, and a Qubit and qPCR machine for DNA quantifications.

The Arima-HiC workflow has one “pre-HiC” quality control assay used to optimize the input material into an Arima-HiC reaction. This protocol is called “Estimating Input Amount” and can be found as a section preceding the Arima-HiC Protocol all of our User Guides. The Arima-HiC kit supplies enough reagent to perform this protocol on 8 samples, one for each reaction in the Arima-HiC kit.

The Arima-HiC workflow has two pre-sequencing quality control steps. Arima-QC1 is to used to assess the quality of proximally-ligated DNA produced by the Arima-HiC protocol, and Arima-QC2 is used to assess the overall experimental quality of the Arima-HiC workflow following library preparation but prior to library amplification. A QC worksheet is provided with the Arima-HiC User Guide to help calculate these QC values. Optional shallow Illumina sequencing can also be performed as a final QC step prior to deeper sequencing.

Arima-HiC libraries can be sequenced using a variety of read lengths offered by Illumina sequencing instruments. In our experience, optimal results are obtained using 2x150bp because longer reads afford higher read mappability, however shorter reads (e.g. 2x36bp) can also be used.

No, Arima Genomics currently does not provide our own software for downstream analysis of sequenced Arima-HiC libraries. For the generation of HiC contact maps and identification and annotation of DNA loops and topological domains, Arima provides support for many open source tools, including Juicer, HiC-Pro, HOMER, HiCUP, and HiC-Bench. For the scaffolding of genomes and de novo assembly applications, initial data processing can be performed using some of the aforementioned tools, as well as the mapping pipeline found on our GitHub page, and we support the contig scaffolding program SALSA.

For several open-source HiC data analysis tools, you will need to have knowledge of the restriction enzyme cut site motifs and/or genomic locations, as well as the possible ligation junction motifs produced by the Arima-HiC chemistry. This information is commonly used for read trimming and downstream HiC data processing. The Arima-HiC chemistry uses restriction enzymes that digest chromatin at ^GATC and G^ANTC, where N can be any of the 4 genomic bases. Our multiple restriction enzyme chemistry produces the following possible ligation junction motifs: GATCGATC, GANTGATC, GANTANTC, GATCANTC. Please contact Technical Support for more information about how to appropriately implement open-source HiC data analysis tools with respect to our HiC chemistry. We will also be happy to share a link to download cut site location files for mouse and human genome builds or help you generate custom cut site location files for your genome of interest.

Yes, Arima Genomics provides comprehensive technical support for both the experimental and analysis portions of Arima-HiC experiments. With respect to data analysis support, the extent of our support is helping users appropriately implement open-source data analysis and visualization tools, and assisting with the quality evaluation of the Arima-HiC data. Arima will also run customers down-sampled Arima-HiC data through internal QC pipelines and provide an assessment of the data quality.