Cart
Products
Arima Promoter Capture HiC Kit Overview
Related Products:
- Arima HiC+ Kit: Visualize 3D genomic interactions.
- Arima High Coverage HiC: Uniform Coverage for Confident Assemblies.
- Arima CiFi Kit: Combine Hi-C and long-read sequencing for complete genome insights.
- ChIP-Seq Assays: Innovative products that make ChIP easier and more successful.
- ATAC-Seq Kits: Genome-wide profiling of open chromatin regions.
Need Assistance? Contact Technical Support
Genome-wide Hi-C shows you the whole 3D genome. Promoter Capture Hi-C zooms in — enriching for the contacts that matter most for gene regulation. The Arima Promoter Capture Hi-C workflow combines the Arima-HiC+ chemistry. with pre-designed biotinylated RNA probes covering a broad, genome-wide collection of annotated gene promoters in human or mouse, delivering high-resolution promoter–enhancer contact maps at ~6× lower sequencing depth than a genome-wide Hi-C experiment.
The Arima Human Promoter Panel covers the promoters of 23,711 genes from the GRCh38 Ensembl v95 annotation (18,741 protein-coding genes plus 4,970 non-coding: antisense, lncRNA, miRNA, snoRNA, snRNA). The Arima Mouse Promoter Panel covers 25,731 genes from GRCm38 Ensembl v94 (21,088 protein-coding plus 4,643 non-coding). In both panels, capture probes are designed to the restriction fragment containing each promoter plus one restriction fragment upstream and one downstream, manufactured with 1× tiling, repeat masking, and balance boosting for uniform enrichment. Over 350,000 RNA baits per panel eliminate the burden of custom design and validation.
On-target performance is engineered to a >60% minimum on-target rate (~20–25× enrichment vs. genome-wide Hi-C), with internal and beta-customer validation routinely exceeding 80% on-target rates. Data are analyzed with the Arima Promoter Capture-HiC+ Pipeline built on the open-source HiCUP and CHiCAGO tools; users supply only the Illumina FASTQ file and Arima supplies all downstream reference files.
Key Features & Benefits
- Genome-wide promoter coverage. 23,711 human genes or 25,731 mouse genes per panel; 350,000+ RNA baits per panel.
- High resolution. 5-kb resolution promoter-anchored contacts across the entire targeted genome.
- Sequencing-efficient. ~100 M paired-end reads per sample, approximately 6× lower depth than a genome-wide Hi-C experiment.
- High enrichment. >60% on-target rate specification (~20–25× enrichment over genome-wide Hi-C); routinely >80% in validation.
- Fast time to data. No custom-design cycle. Panels are pre-manufactured and ready to run.
- Open, optimized analysis. Arima Promoter Capture-HiC+ Pipeline built on HiCUP + CHiCAGO; supply only FASTQ, Arima supplies the rest.
- Broad application. Regulatory-landscape comparison across tissues/samples, disease-variant to target-gene linking, active/inactive promoter interrogation (comprehensive, cell-type-agnostic design).
- Same familiar Hi-C workflow. Built on the 6-hour Arima-HiC+ chemistry and the Arima Library Prep Module.
How the Arima Promoter Capture HiC Kit Works
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.
Arima Promoter Capture HiC Kit Contents
Arima HiC+ Kit
| 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 B | ||
| Enzyme B | ||
| Buffer C | ||
| Enzyme C | ||
| Buffer D | ||
| Enzyme D | ||
| Box C | Enrichment Beads | 2-8°C |
| QC Beads |
Arima Library Prep Module
| 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 Promoter Capture Module
| Box | Reagents | Storage |
|---|---|---|
| Box A | Wash Buffer 1 | 20–25°C |
| Binding Buffer (x3) | ||
| Wash Buffer 2 | ||
| Box B | Fast Hybridization Buffer | −20°C |
| RNAase Block | ||
| Blocker Mix | ||
| Herculase II Fusion DNA Polymerase | ||
| 5X Herculase II Buffer with dNTPs | ||
| Post Capture Primer Mix | ||
| Box C | Streptavidin Beads (T1) | 2-8°C |
Arima Promoter Capture Mouse Probe Module
| Reagents | Storage |
|---|---|
| Arima Mouse Promoter Panel | -80°C |
Arima Promoter Capture Human Probe Module
| Reagents | Storage |
|---|---|
| Arima Human Promoter Panel | -80°C |
Arima Promoter Capture HiC Kit Data
(Click image to enlarge)
Figure 1. pcHi-C reveals distinct SOX2 promoter looping in lung fibroblasts vs. breast cancer cells, showing cell-type-specific gene regulation.
Promoter capture Hi-C (pcHi-C) data compares IMR90 lung fibroblasts with MCF7 breast cancer cells, with blue arcs representing physical loops that connect the SOX2 gene promoter to the regulatory regions controlling it. The looping pattern differs markedly between the two cell types, revealing that the same gene can be activated through entirely different regulatory connections depending on cellular context
(Click image to enlarge)
Figure 2. Multi-omic data links a distal genetic variant to its target gene promoter.
This multi-omic view stacks GWAS association data, ATAC-seq, ChIP-seq, and RNA-seq alongside pcHi-C loop data across the same stretch of DNA, witha highlighted region marking a disease-associated genetic variant and an arc tracing its physical connection to a distal promoter.
Arima Promoter Capture HiC Kit FAQs
Genome wide HiC measures chromatin interactions across the entire genome. Promoter Capture HiC uses biotinylated RNA probes to enrich chromatin interactions involving annotated gene promoters. This targeted approach provides higher resolution at promoters, improves detection of promoter enhancer interactions, and requires about 6× less sequencing than a comparable genome wide HiC experiment.
The human panel targets 23,711 genes from GRCh38 Ensembl v95, including 18,741 protein coding genes, 84 antisense RNAs, 170 lincRNAs, 1,878 miRNAs, 938 snoRNAs, 1,898 snRNAs, and 2 other gene types.
The mouse panel targets 25,731 genes from GRCm38 Ensembl v94, including 21,088 protein coding genes, 207 antisense RNAs, 544 lincRNAs, 1,015 miRNAs, 1,494 snoRNAs, and 1,383 snRNAs.
The probes target the restriction fragment containing each gene promoter, along with one restriction fragment upstream and one downstream. Each panel uses 1× tiling, repeat masking, and balance boosting to support uniform enrichment. Each panel contains more than 350,000 biotinylated RNA baits.
Arima's minimum specification is more than 60% on target reads, corresponding to approximately 20 to 25× enrichment compared with genome wide HiC. Internal validation and beta testing with customer samples have routinely achieved more than 80% on target reads.
Promoter Capture HiC is designed for 5 kb resolution using 100 million paired end reads per sample. This requires approximately 6× less sequencing than a comparable genome wide HiC experiment while providing targeted information about promoter associated chromatin interactions.
Promoter Capture HiC supports cell culture and primary cells, with a standard input of 1 million cells and fresh frozen animal tissues with a standard input of 50-200mg. Lower input amounts may be possible on a case by case basis. Contact Active Motif Technical Support ([email protected]) to discuss your sample requirements.
No. The panels are designed using comprehensive promoter annotations regardless of cell type or cell specific promoter activity. This allows researchers to study chromatin interactions involving both active and inactive promoters across different cell types.
Data are analyzed using the Arima Promoter Capture HiC Pipeline, which incorporates the open source HiCUP and CHiCAGO pipelines. Users provide the Illumina FASTQ files, and Arima provides the required reference files. The analysis generates quality control metrics, chromatin interaction and loop calls, and files that can be visualized in the WashU Epigenome Browser.
Pre designed Promoter Capture HiC panels are available for human hg38 / GRCh38 and mouse mm10 / GRCm38.
For Promoter Capture HiC, we recommend 100 million paired end reads per sample at 2 × 150 bp (PE150) to achieve approximately 5 kb resolution. This sequencing depth is about 6× lower than what is typically required for a comparable genome wide HiC experiment, while providing high resolution information about promoter associated chromatin interactions.
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 Promoter Capture HiC Kit Publications
Reference Protocols:
- Freire-Pritchett, P., Ray-Jones, H., Della Rosa, M., et al. (2021). Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools. Nature Protocols, 16, 4144–4176. https://doi.org/10.1038/s41596-021-00567-5
- Cairns, J., Freire-Pritchett, P., Wingett, S. W., et al. (2016). CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biology, 17, 127. https://doi.org/10.1186/s13059-016-0992-2
Arima Promoter Capture HiC Kit Documents
You might also be interested in:
| Name | Format | Cat No. | Price | |
|---|---|---|---|---|
| Arima Promoter Capture, HiC, Library Kits (human) | 8 rxns | 53251 | $10,475 | Add to Cart |
| Arima Promoter Capture, HiC, Library Kits (mouse) | 8 rxns | 53252 | $10,475 | Add to Cart |
