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Sample Support

The Arima-HiC assay works optimally on cell or tissue samples comprising 3 µg of DNA. For most human cell lines, this usually corresponds to 500,000–1,000,000 cells as input. We have successfully tested the Arima-HiC+ protocol starting with an input of 50,000 crosslinked cells, and our customers have published Arima-HiC+ results for 6,000 double-sorted nuclei (Espeso-Gil, et al. Genome Medicine, 2020).

 

While a cell or tissue sample comprising 3 µg of DNA is the recommended input amount for the Arima-HiC assay, it is possible to produce high-quality Arima-HiC libraries from much fewer cells (e.g. ~50,000 human cells or fewer, depending on the application).

When used to perform the Arima-HiC assay, the Arima-HiC+ kit is compatible with a broad range of sample types, including:

  • Cultured or primary cells
  • Fluorescence-activated cell sorted (FACS) cells/nuclei
  • Fresh tissues preserved in 1) a cryopreservative buffer containing DMSO and/or glycerol and stored at -80˚C, 2) ethanol, stored at -80˚C, and 3) RNAlater™, stored at -80˚C
  • Fresh-frozen bulk animal and plant tissues
  • Fresh, non-frozen, whole blood
  • Fresh nucleated blood preserved in ethanol, stored at -80˚C
The Arima-HiC+ kit is not compatible with:
  • Cultured or primary cells (excluding tissues) that have been frozen without prior crosslinking or without the addition of a cell preservation agent.
  • Harvested tissue with a long time interval between harvest and freezing.
Arima-HiC chemistry is robust and works across a variety of genome compositions. If your genome of interest has unique properties, Arima can run an in silico analysis to inform Arima-HiC assay compatibility.
The Arima-HiChIP assay works optimally on mammalian cells comprising approximately 12 µg of DNA. For most human cell lines, this usually corresponds to 3,000,000–4,000,000 cells as input.
The Arima-HiChIP protocol is compatible with cultured or primary mammalian cells.
The sample input requirements for Arima Capture-HiC are the same as for Arima-HiC. The integrated library prep of the Arima Capture HiC protocol is designed to produce at least 750ng of an amplified proximity ligated NGS library before the capture reaction to ensure a diverse post-capture library. 
Arima’s genome-wide Hi-C technology is applicable to most eukaryotic organisms as exemplified by its extensive utilization for generating chromosome-spanning de novo assemblies for a wide variety of species. Experimental evidence suggests, however, that spatial 3D genome analysis is more challenging to undertake in tissues that contain only a small percentage of nucleated cells, exhibit an extensive extracellular matrix, or contain unique secondary metabolites. Arima Genomics has developed various optimized workflows for different tissues as well as isolated nuclei. Our instructions for crosslinking isolated nuclei and the subsequent Hi-C workflow can be adapted to any species or tissue for which nuclear isolation and enrichment protocols exist. Please contact Arima Genomics Tech Support to evaluate your best experimental options.

Arima’s Custom Capture-HiC+ panels can be designed for non-human samples. The process is more streamlined for the following reference genomes but can be adapted for other targets if necessary: hg19, hg38, mm9, mm10, rn4, TAIR 10, bosTau6, ce6, canFam3, calJac3, dm3, danRer7, galGal3, rheMac2, oryLat2, IRGSP5, sacCer2, S.pombe1.1.

The Arima HiChIP workflow has been most extensively validated for human and mouse samples. Customers planning to apply the Arima HiChIP workflow outside of the validated antibodies or to species other than these 2 model organisms will have to carefully consider the sequence conservation of the antibody target, the host species for the antibody production and the most appropriate antibody capture matrix. Please contact Arima Tech Support to inquire whether we tested a particular antibody or clone for HiChIP.
 
Initially we are releasing the genome-wide promoter capture panels for human and mouse samples. Additional species or different capture panels can be created via our custom capture Hi-C process. If demand for particular panels of high interest emerges or consortia of multiple parties agree on a consolidated design we will consider converting them to off-the-shelf products in the future.
Cost considerations are not one size fits all. Smaller and therefore less expensive capture panels have a lower breakeven point compared to high resolution genome-wide HiC than larger panels. In general, a larger number of samples and the ability to evaluate more replicates of the same condition make capture panels more cost effective. The pre-designed promoter capture panel are the most cost-effective capture panels because they are available at a minimum of 8 reactions, whereas custom capture panels carry a minimum of 16 capture reactions.
The genome-wide promoter panels were designed with comprehensive promoter information from relevant databases, irrespective of cell-specific usage, which should allow for the interrogation of active and inactive promoters. If you are working on newly discovered or secondary promoters, it will probably be useful to check our coverage area relative to your specific areas of interest for overlap. Please contact Arima Tech Support to discuss your needs.

ARIMA-HIC WORKFLOW

Each Arima-HiC+ kit contains 8 reactions. One reaction is typically sufficient for the generation of ~600M raw read-pairs. More precise estimates of library complexity can be determined from the Arima-QC2 assay as outlined in our User Guide.
The Arima-HiChIP protocol involves a 2-day workflow and 1-day library preparation.
Yes, the Arima-HiC+ kit can be used for Capture-HiC studies. For help with Capture-HiC probe design or more information on compatible capture hybridization protocols, please contact technical support.
Yes, the Arima-HiC+ kit can be used for HiChIP and PLAC-seq studies.
Yes. We recommend crosslinking using 2% formaldehyde (See our User Guide for more details.). Crosslinking with different strengths of formaldehyde (e.g., 1%) has also worked with comparable performance; however, we do not recommend using <1% formaldehyde.
Arima currently provides validated Arima HiC+ specific library prep user guides for Swift Accel-NGS™ 2S Plus, KAPA HyperPrep™, Illumina TruSeq™ and NEBNext™ Ultra™ II. For low input applications of the Arima HiC+ and the Arima HiChIP workflows we strongly recommend the Swift protocol. The Arima Capture-HiC+ workflow includes a fully validated and optimized custom library prep module which is required for our enrichment based Hi-C workflow. Please contact an Arima representative to inquire about access to the pre-validated user guides.
We strongly recommend following the Arima User Guide and using 100 µL for shearing. We have validated that shearing in 100 µL of volume in Covaris microtubes produces comparable results to shearing in 130 µL. Perhaps more importantly, the DNA size selection protocol following DNA shearing uses specific SPRI bead-to-sample volume ratios for bead-based size selection. If 130 µL of volume is used as input to the size selection protocol instead of 100 µL, the resulting DNA sizes will be considerably larger than expected and may negatively impact library prep and sequencing performance.
The preparation of Arima-HiC libraries requires a centrifuge for pre-HiC sample prep, a thermomixer or thermal cycler for heated incubations, a Covaris™ or Diagenode™ sonicator for DNA shearing, a thermal cycler for PCR, and a Qubit™ and qPCR machine for DNA quantification.
The requirements for Arima Capture-HiC are the same as for Arima-HiC.
For Capture-HiC, you will follow the Arima-HiC protocol with one modification. This modification is important for generating sufficient material for going into the hybridization step of Capture-HiC and for a quality control sequencing reaction. To generate sufficient material for Capture-HiC hybridization, we recommend splitting the library amplification into 4 reactions. We have found that at higher numbers of PCR cycles the on-bead amplification is less efficient, and by splitting each library into 4 amplification reactions, you will be able to generate sufficient material. The Arima-HiC indexed libraries can be used directly in the Agilent SureSelectXT HS protocol.
We can help you with the bioinformatics to generate probes for your Arima Capture-HiC experiment through our collaborator, Agilent. The probe design with Arima is different for Capture-HiC because we use a multi-enzyme mix, resulting in different cut sites. Arima already has generated probe set sequences in close collaboration with Agilent to look at promoter-specific interaction in human and mice. When using the recommended boosted probe designs with Agilent SureSelectXT HS, a minimum of 500 ng of indexed input DNA is needed. The Arima-HiC indexed libraries can be used directly in the Agilent SureSelectXT HS protocol. We can also help you with designing custom Agilent probe sets for your Arima Capture-HiC experiment in human, mouse, and the reference genomes available in Agilent SureDesign™. For designing a custom Arima Capture-HiC probe set in unsupported or de novo assembled genomes, we can use your target coordinates to generate a target region file that takes into account the Arima cut sites to submit to Agilent Customer Support for probe design. All probe sets will need to be purchased via Agilent.
We recommend using pre-validated custom library prep user guides for Kapa HyperPrep™ or Swift Accel-NGS™ 2S Plus. Please contact an Arima representative to inquire about a pre-validated user guide for your preferred library prep kit.
We recommend using the Accel-NGS™ 2S Plus DNA Library Kit from Swift Biosciences with the Arima-HiChIP kit. 
A 1-mL deep well plate can be used as long as the user can centrifuge at 10,000 x g, and the user can see well enough into the plate to remove the supernatant without disturbing the nuclei pellet.
A lower volume format in PCR plate or strip tube can be used with the following adjustment: 2X with 200 µl of water instead of 1X with 1.5 mL. Plates and tubes must still be centrifuged at 10,000 x g, and the user can see well enough into the plate to remove the supernatant without disturbing the nuclei pellet.
 
We recommend that all buffers be made fresh. The exception is LTE (Tris, low EDTA, TLE) buffer which is commonly stored at room temperature.
 
The samples can be incubated at 25˚C overnight.
Note: In some protocols, samples are incubated at 68˚C overnight to further drive reverse crosslinking.
 
CS Buffer cannot be replaced by Elution Buffer because the SDS concentration is optimized to achieve efficient shearing.
 
We recommend 1000 rpm at 4°C to prevent beads from settling.
Note: A nutator in the fridge may be fine so long as beads do not settle, and the temp is at 4˚C.
 
Arima HiChIP is actively being validated with selected histone and transcription factors. Please contact technical support to determine the current status of your desired antibody.
We recommend the methanol-stabilized formaldehyde.
Note: Using methanol-free formaldehyde might result in reduced crosslinking compared to methanol-stabilized formaldehyde.
 
Arima developed and optimized a restriction enzyme-based proximity ligation chemistry that enriches ligation junctions, does not require the use of a linker oligonucleotide, produces the highest abundance of long-range contact information for regions on the same chromosome and aims to preserve maximum molecular diversity from each sample. It is compatible with a wide range of sample materials and input amounts and has been extensively utilized for the interrogation of the 3-dimensional structure of eukaryotic genomes as well as the chromosome level phased de novo assembly of complex genomes.
Our 2-enzyme chemistry is our most widely utilized option for samples that focus on the spatial organization of genomes, the scaffolding of ne novo assemblies and the identification of large-scale structural variants. The 4-enzyme chemistry improves access to a larger portion of genomes with more extreme GC content and adds utility beyond the spatial genome analysis like phased de novo assembly and comprehensive phased variant calling.
Arima offers both unbiased genome-wide HiC (Arima HiC+) as well as antibody targeted Arima HiChIP to our customers. For fewer numbers of samples and for the comprehensive survey of the whole genome’s spatial organization, the use of Arima-HiC+ is recommended to characterize the status quo and discover differences between conditions. To establish the functional connections between the epigenome (histone modifications, chromatin organizers, transcription factors, etc.) to their spatial organization, the use of Arima HiChIP is recommended. 
Both approaches go hand in hand. It is common to start out discovery with deeply sequenced genome wide HiC to establish a baseline expectation for the spatial organization of a given cell type/condition. Once specific regions of interest are established and larger sample numbers need to be processed, Capture HiC would allow much better scalability of a project. It is also possible to sequence a portion of the genome-wide HiC library while retaining the majority for Capture HiC. As a middle ground for targeted discovery, Arima Genomics developed and released genome-wide promoter capture panels for human and mouse samples.
With the availability of semi-custom capture panels from Arima Genomics, it is now possible to interrogate specific regions of interest via Capture HiC. This approach allows the characterization of 3D interactions in the presence and absence of epigenetic marks and is therefore preferred to study changes in the 3D genome. If the goal of the project is to correlate the 3D genome with its activity state, target 3D interaction analysis to certain activity states of the genome or establish whether certain (sub)components or epigenetic marks are associated with specific 3D structures, HiChIP would be the preferred option.
Arima released a fully integrated Arima Capture HiC workflow that is based on the Arima HiC+ chemistry, incorporates important improvements for optimizing your capture HiC results and includes not only the HiC proximity ligation module, but also an optimized library prep module that includes sample indices as well as the capture chemistry and probes. Please contact sales@arimagenomics.com to discuss your capture needs as well as pricing and availability. For technical and workflow inquiries please contact techsupport@arimagenomics.com
We provide an end-to-end capture HiC workflow which includes complete instructions for crosslinking, HiC chemistry, shearing, library prep, QC and the capture module in various workflow-specific user guides, making modifications to the Arima HiC+ protocol unnecessary.
We can help you with the bioinformatics to generate optimized probes for your Arima Capture-HiC experiment. Target region design for Arima Capture HiC is different than general hybridization capture panels because we use multiple restriction enzymes which produce various ligation junctions. Our probe design process was developed to preferentially place probe sequences near restriction sites and avoids regions unproductive for HiC analysis. We currently have predesigned genome-wide promoter capture Hi-C panels available for human and mouse. We can also help you design semi-custom panels for Arima Capture-HiC+ for the following genomes: (hg19,hg38,mm9,mm10,rn4,TAIR 10,bosTau6, ce6,canFam3,calJac3,dm3,danRer7,galGal3,rheMac2,oryLat2,IRGSP5,sacCer2,S.pombe1.1). If you require custom capture panel designs for other reference genomes, please contact techsupport@arimagenomics.com
Our fully integrated Arima Capture-HiC+ products include a validated and optimized library prep module that includes 16 Illumina™ compatible indices for sample multiplexing with the kit.
The Arima Technology Platform is currently only available for research use only. However, some of Arima Genomics clinical research customers have been able to utilize Arima HiC technologies to establish deviations in the 3D genome as the root cause for specific subtypes of diseases, gain mechanistic insights into the interplay of the spatial conformation of the genome and pathological processes or utilize 3D genome information as a novel disease classifier. Any customer interested in utilizing Arima Genomics technologies for either lab developed tests (LDT) or plans to develop and seek FDA authorization of in vitro diagnostic devices (IVD) is urged to contact Arima Genomics to evaluate the support our team can provide.
The Arima Capture HiC protocol has been extensively optimized to exceed 80% on target rates and provide a seamless workflow to our customers while adding only 1 day for the capture workflow. Publicly available workflows are typically provided for specific project-related samples and do not come with detailed instructions for crosslinking, HiC workflow, shearing, library prep to the capture module and bioinformatics support. Existing capture panels will only have limited utility for our 2 restriction enzyme based Hi-C chemistry due to the workflow-specific ligation junctions created during the Arima Hi-C process. Taking the predicted restriction enzyme recognition sites into consideration during probe design allows us to better tailor our custom capture product to the customer’s needs.
We have only limited internal experience in targeting non-coding GWAS hits via our Capture HiC product to identify their interacting genes. If you would like to discuss such a project with our Tech Support scientists, it would be important to mine the nearby regions around the GWAS hits for putative enhancer signatures or other epigenetic signatures to determine how far to expand the capture region around each variant locus.

QUALITY CONTROL

The Arima-HiC workflow has one “pre-HiC” quality control assay used to optimize the input material into an Arima-HiC reaction. This protocol is called “Estimating Input Amount” and can be found as a section preceding the Arima-HiC protocol in all of our User Guides. The Arima-HiC kit supplies enough reagent to perform this protocol on 8 samples, one for each reaction in the Arima-HiC kit.
The Arima-HiC workflow has two pre-sequencing, quality control steps. Arima-QC1 is used to assess the quality of proximally ligated DNA produced by the Arima-HiC protocol, and Arima-QC2 is used to assess the overall experimental quality of the Arima-HiC workflow following library preparation but prior to library amplification. A QC worksheet is provided with the Arima-HiC User Guide to help calculate these QC values. Optional, shallow, Illumina sequencing can also be performed as a final QC step prior to deeper sequencing.
The Arima-HiChIP workflow has one “pre-HiC” quality control assay used to optimize the input material into an Arima-HiChIP reaction. This protocol is called “Estimating Input Amount” and can be found as a section preceding the Arima-HiChIP protocol in all of our User Guides. The Arima-HiC kit supplies enough reagents to perform this protocol on 8 samples, one for each reaction in the Arima-HiC kit.
The Arima-HiChIP workflow has three pre-sequencing quality control steps and two post-sequencing data QC steps. A QC worksheet is provided with the Arima-HiC+User Guide to help calculate these QC values.  
 
Focusing your sequencing budget on your regions of interest is the goal of capture Hi-C, but for samples that have not been previously characterized via genome-wide Hi-C, there is the possibility that major interference or deviations are being missed by the targeted Hi-C approach. For instance, large scale structural deviations (translocations, inversions, duplications) that involve your region of interest can be identified by shallow sequencing the pre-capture library. In addition, the pre-capture shallow sequencing data allows the researcher to calculate enrichment efficiency of the capture process. From a data QC perspective, it is very useful to characterize the diversity and quality of the pre-capture library via shallow sequencing to ensure only samples of sufficient quality and diversity are being subjected to capture.
Arima established a minimum on-target rate of >60%, which is ~20-25X fold enrichment over genome-wide HiC. Our internal validation efforts as well as our beta customers for this product have routinely exceeded 80% on-target rates for our test samples and some of their user-provided samples.

ANALYSIS

Arima-HiC libraries can be sequenced using a variety of read lengths offered by short read sequencing instruments. In our experience, optimal results are obtained using 2 x 150 bp for the majority of applications, because longer reads afford higher read mappability, with the minimum read length being 2 x 36 bp and 2 x 250 bp used for phased de novo assemblies of diploid genomes (Garg, et al. Nature Biotechnology, 2020).
We do not provide our own software for downstream analysis of sequenced Arima-HiC libraries. For the generation of HiC contact maps and identification and annotation of DNA loops and topological domains, we can provide support for a limited number of open-source tools but strongly recommend the use of the Juicer/Juicer Tools pipeline (https://github.com/aidenlab/juicer/wiki). Juicer’s use of the BWA aligner is best suited to map chimeric reads efficiently. Other bowtie-based analysis tools (HiC-Pro, HiCUP, and HiC-Bench) have been successfully used by our customers as well. For genome scaffolding, initial data processing for QC can also be performed using Juicer; we recommend read mapping to be performed via our mapping pipeline found on our GitHub page (https://github.com/ArimaGenomics/mapping_pipeline), followed by our preferred contig scaffolding program, SALSA (https://github.com/marbl/SALSA). Arima High-Coverage HiC is a critical component of the DipAsm assembly algorithm for phased de novo assemblies of diploid genomes (https://github.com/shilpagarg/DipAsm).
For several open-source Hi-C data analysis tools, you will need to have knowledge of the restriction enzyme cut site motifs and/or genomic locations, as well as the possible ligation junction motifs produced by the Arima-HiC chemistry. This information is commonly used for read trimming and downstream Hi-C data processing. The Arima-HiC chemistry uses restriction enzymes that digest chromatin at ^GATC and G^ANTC, where N can be any of the 4 genomic bases. Our multiple restriction enzyme chemistry produces the following possible ligation junction motifs: GATCGATC, GANTGATC, GANTANTC, GATCANTC. Please contact technical support for more information about how to appropriately implement open-source Hi-C data analysis tools with respect to Arima-HiC chemistry. We will also be happy to share a link to download cut site location files for mouse and human genome builds or help you generate custom cut site location files for your genome of interest.
Yes, we provide comprehensive technical support for both the experimental and analysis portions of Arima-HiC experiments. We can help users implement our preferred open-source data analysis and visualization tools (Juicer for HiC and MAPS for HiChIP) and assist with the quality evaluation of the Arima-HiC data. We will also run customers’ down-sampled Arima-HiC data through our internal QC pipelines (Juicer for HiC and MAPS for HiChIP) and provide an assessment of the data quality.
For a mammalian genome of 3 Gb, we recommend sequencing two biological replicates per biological condition. For high-resolution analysis of A/B compartments, topologically associating domains (TADs), and chromatin loops, the desired read depth is >600 million paired-end reads for each replicate.  For shallow sequencing used in library QC, we recommend at least 1 million paired-end reads.
When capturing long continuous regions via Arima Capture-HiC+, it is recommended to generate at least 10M paired end reads for each 1Mb of probe covered region. For promoter capture or disjointed target regions the maximum or most cost-effective sequencing depths for a given panel and sample combination should be empirically determined via shallow sequencing of test libraries to optimally plan the deep sequencing capacity of each library according to its estimated library diversity. The Juicer pipeline conveniently calculates this diversity estimate automatically.
 
We tested HiCUP (bowtie) in combination with CHiCAGO and ChiCMaxima for region-specific 3D loop analysis at different genomic bin sizes and coverage levels. Our internal analysis comparisons against a ground truth set determined that a combination of HiCUP and CHiCAGO produced the most replicate concordant and sensitive results for our standard GM12878 sample for our genome-wide promoter capture HiC product. It is still possible that different experimental conditions will benefit from a different combination of analysis tools. To support basic data analysis needs, we are making an Arima Capture HiC bioinformatics user guide available to our customers. We are also hosting an integrated Arima-specific capture HiC analysis pipeline on our Github page. In addition to the instruction, we are also making all the required input and auxiliary files for our promoter capture panels (baitmaps, rmaps, design files, reference genomes, settings files) available via our anonymous FTP server.


Baitmap and fragment files for mouse and human are available for download. Please contact customer support for details. 
 
We will gladly help you generate the baitmap file for your Arima Capture-HiC experiment. The baitmap file is generated by intersecting the covered region data from your capture probeset with the fragment file of your reference genome/contigs. The fragment file is generated by in silico digestion of your reference genome/contigs with the Arima-specific restriction enzyme cut sites.
We provide detailed recommendations for estimating the optimal Arima-HiChIP sequencing depth to produce robust and reproducible chromatin loop discovery using the MAPS data analysis pipeline. The optimal sequencing depth depends on the number of reads that can be used to identify chromatin loops and the desired resolution of the chromatin looping analysis. For shallow sequencing used in library quality control, we recommend at least 500,000 paired-end reads.

For analysis of Arima HiChIP data, we recommend the Arima-MAPS 2.0 tool. The latest update is available here (https://github.com/ijuric/MAPS), and the original MAPS pipeline is available here (https://github.com/ijuric/MAPS/releases/tag/v1.1.0).  Benchmarking with MAPS, FitHiChIP, HICCUPS, and CriSPRi-validated genomics loops revealed that MAPS has the highest sensitivity with a moderate false-positive rate while minimizing computational time. The MAPS 2.0 pipeline has been updated to include the MACS2 ChIP-seq peak calling algorithm, which allows ChIP-seq peak calling from Arima-HiChIP data as well as improved usability by the expansion of command line options.

A test dataset to verify the Arima-MAPS installation and configuration is available at ftp://ftp-arimagenomics.sdsc.edu/pub/MAPS/test_data/.

Yes.  The Arima-MAPS tool requires a configuration file, a ChIP-Seq peak file generated from the same cell type and antibodies, and a genomic features file. If no HiChIP reference peaks are available from your ChIP experiments, ENCODE sources multiple alternative ChIP peaks for various chromatin proteins.
The files needed to run Arima-MAPS are available at https://github.com/ijuric/MAPS/tree/master/Arima_Genomics/.

A test dataset to verify the MAPS installation and configuration is available at ftp://ftp-arimagenomics.sdsc.edu/pub/MAPS/test_data/.
Yes! Please view our latest bioinformatics user guide for Arima-HiC+ and Arima High Coverage HiC here.
Arima has optimized the Hi-C workflow to significantly reduce non-specific inter-chromosomal contacts, improve the on-target rate of the capture assay, reduce experimental noise and thereby lower the number of false positives from spurious off-target signals. Arima’s promoter capture Hi-C product is designed to only characterize long range DNA contacts that may impact regulation through promoter-interactions, which also contributes to fewer loop calls in off-target regions. Capture Hi-C results are typically combined with other functional genomics data sets (like RNA-seq, ChIP-seq or ATAC-seq) to identify functionally relevant 3D interactions among the many that are reported.
Our pipelines currently do not support differential loop calling out of the box. They do provide a visual representation of loop calls to help you compare different samples. Due to the rapidly changing options and significant interest by algorithm developers on differential loop calling we would like to refer our customers to this frequently updated list of other open-source analysis algorithms: https://github.com/mdozmorov/HiC_tools#differential-interactions.