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Arima High Coverage HiC Kit

Uniform Coverage for Confident Assemblies.

 

Arima High Coverage HiC Kit Overview

Arima High Coverage HiC KitArima High Coverage HiC Kit
Arima Library Prep KitArima Library Prep Kit
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The Arima High Coverage HiC Kit extends Arima's proximity-ligation chemistry with a four-enzyme restriction cocktail engineered to access a substantially larger fraction of the genome than 2-enzyme Hi-C The added coverage uniformity makes this kit the preferred Hi-C input for phased de novo assembly.

Like Arima-HiC+, the High Coverage HiC workflow captures both the sequence and 3D conformation of the genome in a single assay. Where Arima-HiC+ is optimized for genome-wide 3D architecture (compartments, TADs, loops), Arima High Coverage HiC is the choice when your project depends on per-base coverage uniformity, for example, when ordering and orienting contigs, fixing mis-assemblies, indentifing structural variants and phasing haplotypes.

Key Features & Benefits

  • Four-enzyme chemistry for uniform per-base coverage. Accesses AT-rich, GC-rich, and repetitive regions that are underrepresented with 2-enzyme Hi-C.
  • Purpose-built for phased de novo assembly. Purpose-built for phased de novo assembly using hifiasm and the DipAsm workflow. Supports haplotype-resolved diploid assemblies using PacBio HiFi reads with Hi-C-based phasing (Cheng et al., Nature Methods 2021; Garg et al., Nature Biotechnology 2020)
  • Same 6-hour proximity-ligation workflow and QC framework as Arima-HiC+, a familiar experience for existing Arima users.
  • Broad sample compatibility. Cell lines, fresh-frozen animal tissue, plant tissue, PBMCs, cryopreserved cells, whole nucleated blood.
  • Full downstream pipeline. Compatible with the Arima mapping pipeline and widely used downstream workflows, including YaHS, SALSA2, and 3D-DNA for Hi-C–based genome scaffolding; hifiasm and DipAsm for de novo, haplotype-resolved genome assembly using long reads with Hi-C data; and Juicer, HiC-Pro, and Juicebox for Hi-C data processing, contact-map generation, visualization, and 3D-genome analysis.
  • 8- and 48-reaction formats to support single-sample projects and consortium-scale programs alike.

Arima High Coverage HiC is an experimental workflow that captures the sequence and structure (three-dimensional conformation) of genomes. As illustrated in the Arima High Coverage HiC workflow schematic above, chromatin from a sample source (tissues, cell lines, or blood) is first crosslinked to preserve the genome sequence and structure. The crosslinked chromatin is then digested using a 4-restriction enzyme (RE) cocktail optimized for coverage uniformity across a wide range of genomic sequence compositions. The 5’- overhangs are then filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA are ligated, capturing the sequence and structure of the genome. The ligated DNA is 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 High Coverage HiC Kit Works

How the Arima High Coverage HiC Kit Works

 

Arima High Coverage HiC Kit Contents

Arima High Coverage HiC Kit Contents (Cat. No. 53231 & cat. No. 53232):

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 F
Enzyme F1
Enzyme F3
Enzyme F4
Enzyme A2
Buffer G
Buffer C
Enzyme B
Enzyme C
Enzyme D
Box C Enrichment Beads 2-8°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 High Coverage HiC and Library Prep Kits (Cat. No. 53239 & cat. No. 53240):

The bundle includes the components of the Arima High Coverage HiC kit and the library preparation kit.



 

Arima High Coverage HiC Kit Data

Hi-C contact maps before and after scaffolding
(Click image to enlarge)

Figure 1. Hi-C contact maps before and after scaffolding with High Coverage Hi-C data.
Left: Hi-C map for contigs. Hi-C read pairs are mapped onto unordered input contigs, concatenated in arbitrary order along both axes. A high density of off-diagonal contacts is visible throughout the map. These represent true 3D chromatin contacts between contigs that are actually adjacent or nearby on the same chromosome, but which have not yet been correctly ordered and oriented in the assembly. The scattered signal reflects the fragmented state of the input contig set prior to scaffolding

Right: Scaffolded assembly using high coverage Hi-C data. After scaffolding with a high depth of Hi-C read pairs, the contact signal resolves into discrete blocks along the diagonal, each corresponding to an individual chromosome. Contact density is highest near the diagonal and decays with genomic distance, consistent with the physical principle underlying Hi-C: chromatin loci that are closer together in the nucleus are captured by proximity ligation more frequently than distal loci. Long-range read pairs provide valuable linkage information for distinguishing true contig adjacencies from background noise, supporting accurate contig ordering and orientation across repetitive or structurally complex regions. The clean, block diagonal structure, with minimal off-diagonal noise, demonstrates that high coverage Hi-C data enables accurate, chromosome scale scaffolding, resolving the ambiguity present in the contig level map.


 

Arima High Coverage HiC Kit FAQs

Both the Arima HiC+ Kit and Arima High Coverage HiC Kit use Arima’s proximity ligation technology and the same 6-hour, 8-step workflow for Hi-C sequencing library preparation.

The 2-enzyme Arima HiC+ chemistry is optimized for studying 3D genome organization, including chromatin compartments, topologically associating domains (TADs), chromatin loops, and detection of large-scale structural variants.

The 4-enzyme Arima High Coverage Hi-C chemistry is designed to improve genome accessibility, including in regions that may be less accessible with single-enzyme and 2-enzyme approaches. By generating more broadly distributed Hi-C junctions across the genome, it supports contig scaffolding, ordering and orientation, assembly validation, and haplotype phasing. It is well suited for applications requiring more complete genome representation, from de novo assembly and genome polishing to haplotype-resolved analysis

The Arima High Coverage HiC Kit supports a wide range of sample types, including fresh-frozen animal tissue, PBMCs, cultured cells, FACS-sorted cells, cryopreserved cells, whole nucleated blood, and fresh-frozen plant tissue.

Recommended input amounts include:

  • Fresh-frozen animal tissue: 50 to 200 mg standard input; less than 50 mg or less than 50 µL for low-input samples
  • PBMCs: collected from at least 2 mL whole blood
  • Cell culture cells: at least 1 million cells standard input; less than 1 million cells for low-input samples
  • FACS-sorted cells: compatible with low-input workflows
  • Cryopreserved cells: compatible
  • Whole nucleated blood: approximately 25 µL
  • Fresh-frozen plant tissue: 2 to 3 g

The Arima High Coverage HiC reaction is optimized for crosslinked samples containing 500 ng to 5 µg of DNA. Less than 500ng of DNA may be used depending on sample type, quality and application .

Arima recommends paired-end 150 bp sequencing (PE150) on Illumina sequencing platforms.

Recommended sequencing depth depends on the application: For genome scaffolding of a ~3 Gb genome, up to 600 million read pairs (~60× coverage) are recommended.

For smaller genomes, sequencing depth can be adjusted up to approximately 200 million read pairs per gigabase of genome size.For 3D genome analysis of a genome approximately 3 Gb in size, a minimum of 600 million paired-end reads per biological condition is recommended. Alternatively, 300 million paired-end reads per biological replicate can be used for two biological replicates.

No. Illumina-compatible library preparation reagents are not included with the Arima High Coverage HiC Kit and must be purchased separately.

The Arima Library Prep Module (Set 1-16, cat. No. 53243 & Set 17-32, cat. No. 53244, 16 reactions) contains the reagents required for T1 streptavidin bead-based enrichment, end repair, dA-tailing, adapter ligation, and 16 unique Illumina-compatible dual-index primer pairs.

Arima High Coverage HiC sequencing data can be analyzed using commonly used Hi-C bioinformatics tools.

For genome scaffolding, Arima High Coverage Hi-C data can be processed with Arima’s public mapping pipeline and used with scaffolding tools such as YaHS, SALSA2, and 3D-DNA.

For haplotype-resolved de novo genome assembly, Arima High Coverage Hi-C data can be used with tools such as hifiasm and DipAsm

For 3D genome analysis, supported tools include Juicer, HiC-Pro, and Juicebox.

Restriction enzyme cut-site files and ligation junction motifs specific to the 4-enzyme Arima High Coverage HiC chemistry are available through Active Motif Technical Support.

The Arima Hi-C workflow includes quantitative pre-sequencing quality control steps to evaluate sample performance before deep sequencing.

Arima-QC1 measures post-ligation biotin incorporation efficiency.

An optional shallow Illumina sequencing step of approximately 1 million reads can be used as an additional quality control checkpoint before high-depth sequencing depending on genome quality.

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 High Coverage HiC Kit Publications

Reference Protocols:

 

Arima High Coverage HiC Kit Documents

 


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Arima High Coverage HiC Kit 8 rxns 53231 $3,475 Add to Cart
48 rxns 53232 $20,840 Add to Cart
Arima High Coverage HiC and Library Prep Kits 8 rxns 53239 $4,470 Add to Cart
16 rxns 53240 $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
Bioinformatics User Guide for Arima-HiC+ and Arima High Coverage HiC
User Guide: Arima High Coverage HiC Kit
User Guide: Library Preparation for Arima High Coverage HiC Kit
Application Note: The Role of Hi-C in Genome Assembly
Product Flyer: The Arima-HiC Kit for Reproducible 3D Genome Conformation Analyses
Worksheet Arima High Coverage HiC – Quality Control