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Arima HiC+ Kit Overview
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Need Assistance? Contact Technical Support
The Arima-HiC+ Kit is a proximity-ligation kit engineered to make robust, publication-quality Hi-C accessible in any molecular biology lab. Chromatin from your sample is crosslinked to preserve its 3D conformation, digested with a proprietary restriction-enzyme (RE) cocktail optimized for uniform genome coverage, filled in with biotinylated nucleotides, and ligated at spatially proximal ends. The resulting proximally-ligated DNA is purified, enriched on streptavidin beads via the Arima Library Prep Module, and sequenced paired-end on Illumina platforms. Downstream, open-source tools (Juicer, Juicebox, HiC-Pro) resolve A/B compartments, topologically associating domains (TADs), and chromatin loops.
The workflow was designed for first-time Hi-C users as well as experienced 3D-genomics labs. It streamlines Hi-C to a 6-hour, 8-step protocol with ~1 hour hands-on time and integrates quantitative pre-sequencing QC (Arima-QC1 and shallow sequencing QC) so you know your library is publication-ready before you commit to deep sequencing.
Key Features & Benefits
- Uniform genome-wide coverage. Multi-restriction-enzyme chemistry (cutting at ^GATC and G^ANTC) delivers uniform coverage across ~90% of the genome, avoiding the ~30% of the genome that is often inaccessible with single-4-cutter Hi-C.
- Rapid, streamlined workflow. 6-hour, 8-step protocol with 1 hour hands-on time; single-tube, 96-well plate compatible; automation friendly.
- Broad sample compatibility. Validated for cultured/primary cells, FACS-sorted cells/nuclei, fresh and frozen animal and plant tissues, PBMCs, cryopreserved cells, whole nucleated blood (fresh or ethanol-preserved), and FFPE tissue (with the Arima-HiC+ FFPE variant).
- Low input support. Optimal input is 500 ng–5 µg DNA (typically 500,000–1,000,000 human cells), with successful published Hi-C from fewer cells (Romero, MA et al BioRxV, 2026) and double-sorted nuclei (Espeso-Gil et al., Genome Medicine 2020).
- Quantitative QC built in. Arima-QC1 (post-ligation biotin incorporation) lets you filter samples before library preparation.
- Sequencing efficient. 1 reaction produces libraries complex enough for up to ~600 M read-pairs — enough for genome-wide 5-10kb loop calls in a mammalian genome.
Arima-HiC is an experimental workflow that captures the sequence and structure (three-dimensional conformation) of genomes. As illustrated in the Arima-HiC workflow schematic above, crosslinked chromatin in customer provided crosslinked cells was digested using a 2-restriction enzyme (RE) cocktail. The 5’-overhangs were filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA were ligated, capturing the sequence and structure of the genome. The ligated DNA was then purified, producing pure proximally-ligated DNA. The proximally-ligated DNA was fragmented using the Bioruptor Pico from Diagenode or the PIXUL sonicator from Active Motif, and the biotinylated fragments were enriched using Streptavidin beads. The enriched fragments are then subjected to a custom library preparation protocol utilizing Arima Library Prep Module (Cat. No. 53243, indexes 1-16; Cat. No. 53244, indexes 17-32) to produce Arima-HiC libraries for sequencing.
How the Arima HiC+ Kit Works
Arima HiC+ Kit Contents
Arima HiC+ Kit (Cat. No. 53233):
| Box | Reagents | Storage |
|---|---|---|
| Box A | Stop Solution 1 | 20–25°C |
| Elution Buffer | ||
| Wash Buffer | ||
| Conditioning Solution | ||
| Stop Solution 2 | ||
| Buffer D | ||
| Buffer E | ||
| Box B | Lysis Buffer | −20°C |
| Buffer A | ||
| Enzyme A1 | ||
| Enzyme A2 | ||
| Buffer C | ||
| Enzyme B | ||
| Buffer B | ||
| Enzyme C | ||
| Enzyme D | ||
| Box C | Enrichment Beads | 4°C |
| QC Beads |
Arima Library Prep Module (Cat. No. 53243 & cat. No. 53244):
| Box | Reagents | Storage |
|---|---|---|
| Box A | End A Buffer | -20°C |
| End Repair A Tailing Enzyme mix | ||
| Ligation Buffer | ||
| T4 DNA Ligase | ||
| Adaptor Oligo Mix | ||
| Herculase II Fusion DNA Polymerase | ||
| 5x Herculase II Buffer with dNTPs | ||
| Box B | Indexes Strip Tubes (1-16) | −20°C |
| Box C | Streptavidin Beads (T1) | 2-8°C |
| Box D | Binding Buffer | 20–25°C |
Arima HiC+ and Library Prep Kits (cat. No. 53242 & cat. No. 53243)
The bundle includes the components of the Arima HiC+ kit and the library preparation kit.
Arima HiC+ Kit Data
(Click image to enlarge)
Figure 1. Hi-C contact matrix (example below) visualizes all pairwise chromatin interactions across the genome.
Brighter dots indicate higher contact frequency between two genomic loci. The off diagonal dots highlight specific long range loops, revealing how distant regions of the linear genome fold together in 3D space.
(Click image to enlarge)
Figure 2. Examples of chromosome-wide Hi-C heatmap and compartment eigenvector.
Zoomed in view to the entirety of chromosome 7. In the chromosome-wide Hi-C heatmap, compartment signal is observed in the data as a checkered pattern, which corresponds to alternating blue and red signal in the compartment eigenvector track on the left and top of the heatmap. The A/B compartment signal, from Juicer Eigenvector, plotted in wiggle format in blue and red is on both axis.
(Click image to enlarge)
Figure 3. Example Hi-C heatmap of identified topologically associating domains (TADs).
Hi-C contact map of chromosome 3 from ~50–85 Mb. TADs are regions of the genome with enriched local chromatin interactions and appear as triangular blocks of increased contact frequency along the diagonal of the Hi-C matrix. Computationally identified TAD boundaries are overlaid as yellow triangles on the lower-left half of the matrix, while the upper-right half is left unobstructed to provide a clearer view of the underlying Hi-C interaction data.
Arima HiC+ Kit FAQs
The Arima HiC+ protocol takes approximately 6 hours and consists of 8 workflow steps with only ~1 hour of hands-on time. Library preparation is then completed using the Arima Library Prep Module.
The Arima HiC+ assay performs optimally with samples containing 500 ng to 5 µg of DNA, which typically corresponds to 500,000–1,000,000 human cells. Published studies have also demonstrated successful lower amounts of cells, ask [email protected] for more details.
The Arima HiC+ Kit is compatible with a wide range of sample types, including cultured cells, primary cells, FACS-sorted cells or nuclei, fresh and fresh-frozen animal tissues, plant tissues, PBMCs, cryopreserved cells, and whole nucleated blood (fresh or ethanol-preserved at −80 °C). The kit is not recommended for cells frozen without prior crosslinking or preservation or for tissues that experienced prolonged delays between collection and freezing.
Recommended sequencing depth depends on your research objective.
600 million paired-end reads per biological condition
Ideal for high-resolution analysis of chromatin loops, topologically associating domains (TADs), and A/B compartments in mammalian genomes (~3 Gb).
300 million paired-end reads
Recommended for standard-resolution analysis of chromatin compartments and TADs.
100–150 million paired-end reads
Suitable for structural variant detection.
1 million paired-end reads
Sufficient for shallow sequencing quality control of Hi-C libraries before deep sequencing.
The recommended sequencing format is 2 × 150 bp paired-end sequencing.
The Arima HiC+ workflow has been validated with several library preparation kits, including Arima Library Prep Module, KAPA HyperPrep, Illumina TruSeq, and NEBNext Ultra II. The Arima Library Prep Module is recommended for optimal performance and is required for the complete Arima Capture HiC+ workflow.
Contact map generation
Juicer (recommended), HiC-Pro
Visualization
Juicebox
Genome scaffolding
YaHS, SALSA2, 3D-DNA
Arima also provides restriction enzyme cut-site files and Arima-specific ligation junction motifs (GATCGATC, GANTGATC, GANTANTC, GATCANTC) through Active Motif Technical Support.
If you need assistance at any time, please call or send an e-mail to Active Motif Technical Service at one of the locations listed below.
North America
Email: [email protected]
Phone: Toll Free - 877 222 9543
Phone: Direct - 760 431 1263
Fax: 760 431 1351
Europe
Email: [email protected]
Phone: Direct: +32 (0)2 653 0001
Fax: +32 (0)2 653 0050
Japan
Email: [email protected]
Phone: +81 (0)3 5225 3638
Fax: +81 (0)3 5261 8733
China
Email: [email protected]
Phone: (86)-21-20926090
Arima HiC+ Kit Publications
Reference Protocols:
- Espeso-Gil, S., et al. (2020). A chromatin connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons. Genome Medicine, 12, 114. https://doi.org/10.1186/s13073-020-00799-2
- Dixon, Jesse R., et al. (2018). Integrative detection and analysis of structural variation in cancer genomes using high-throughput sequencing and Hi-C (hic_breakfinder). Nature Genetics, 2018.
- Wingett, Steven, et al. (2015). HiCUP: Pipeline for mapping and processing Hi-C data. F1000Research, 4, 1310.
- Durand, Neva C., et al. (2016). Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems, 3(1), 95–98.
Arima HiC+ Kit Documents
You might also be interested in:
| Name | Format | Cat No. | Price | |
|---|---|---|---|---|
| Arima HiC+ Kit | 8 rxns | 53233 | $3,475 | Add to Cart |
| Arima HiC+ and Library Prep Kits | 8 rxns | 53241 | $4,470 | Add to Cart |
| 16 rxns | 53242 | $7,740 | Add to Cart | |
| Arima Library Prep Kit, Set 1 (Indexes 1-16) | 16 rxns | 53243 | $1,205 | Add to Cart |
| Arima Library Prep Kit, Set 2 (Indexes 17-32) | 16 rxns | 53244 | $1,205 | Add to Cart |
