Arima-HiC+ for promoter cHiC (human)

Complete Kit to capture human promoter sequences from Arima HiC libraries using the Arima Capture-HiC Workflow

Product Description

The Arima Capture-HiC+ platform technology enables researchers to characterize the spatial, 3-dimensional properties of genomic regions of interest. Researchers now have the ability to compare and contrast the regulatory landscape of different tissues/samples with Promoter Capture using the Arima Capture-HiC Workflow described below.

Kit components:

• Arima HiC+ Kit (Cat# A51008-ARI)
• Arima Promoter Capture module (human) (Cat# A302010-ARI)
• Arima Library Prep Module (Cat# A303011-ARI)

*Other sample types are possible based

**Lower input amounts are possible; contact us for more information.

Arima Capture-HiC Workflow:

Arima Capture-HiC is an experimental workflow that captures the sequence and structure (threedimensional conformation) of genomes. Arima Capture-HiC has been successfully performed on a wide-range of species from the plant and animal kingdoms. Chromatin from the sample source (tissues, cell lines, or blood) is first crosslinked to preserve the genome sequence and structure. Using the Arima HiC+ Kit the crosslinked chromatin is then digested with a restriction enzyme (RE) cocktail. 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 is then fragmented, and the biotinylated fragments are enriched. The enriched fragments are then subjected to a custom library preparation protocol utilizing the Arima Library Prep Module. The interactions of interest are enriched using biotinylated RNA probes from the Arima Human Promotor Panel.

Human Promoter Panel Probe Design:

The Arima Human Promoter Capture Probes were made to the promoters of 23,711 genes from the human GRCh37 Ensemble database, version 87, including: 18,741 protein-coding genes, 84 antisense RNA’s, 107 lincRNA’s, 1,878 miRNA’s, 938 snoRNA’s, and 1,898 snRNA’s. Capture probes were designed to the restriction fragment of each of the promoters as well as to one restriction fragment up-stream and one fragment downstream of the fragment containing the promoter. The probes were manufactured using 1x tiling with repeat masking and balance boosting.

Sequencing and Data Analysis:

Arima Capture-HiC libraries are sequenced via Illumina sequencers in “paired-end” mode. The resulting data is referred to as Arima Capture-HiC data. The tools necessary for analyzing and visualizing Arima Capture-HiC data are included in the Arima Capture-HiC Analysis Pipeline. The pipeline has precomputed a number of files needed for alignment and loop calling for samples captured with the Arima Human Promoter Panel. Finally, the pipeline outputs a number of files which enable an assessment of quality of the Capture-HiC libraries as well as visualizations for viewing and comparing loop calls from different samples.