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.

 

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.

rima-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