rhAmpSeq™ CRISPR Panels

Highly multiplexed, targeted amplicon sequencing for critical analysis of your CRISPR edits

The rhAmp™ primer pairs in rhAmpSeq CRISPR Panels mitigate primer dimers and maximize multiplexing to provide you with high-quality amplicon libraries. Analyze more samples faster with the confidence of uniform coverage and the time savings of efficient library prep. The rhAmpSeq Design Tool makes it easy to input your targets, and our speedy delivery means you can assess your CRISPR results sooner.

Ordering

With our rhAmpSeq CRISPR Panels you have several advantages:

Interrogate CRISPR edits in a variety of species with your own custom panel
Multiplex hundreds of primer pairs in a single pool
Select from a flexible set of delivery scales and formats

rhAmpSeq CRISPR Panels

Create custom NGS amplicon panels.

Design and order

To complete your rhAmpSeq CRISPR Analysis System workflow, you will also need the rhAmpSeq CRISPR Library Kit and rhAmpSeq Index Primers. The rhAmpSeq CRISPR Library Kit includes Analysis Credits to enable data processing and quantification of editing events with the rhAmpSeq CRISPR Analysis Tool.

Product Details

rhAmpSeq CRISPR Panels are highly multiplexed primer sets for targeted sequencing. These panels have been expressly designed for a wide range of species. They are Custom rhAmpSeq Panels specifically designed to assess CRISPR edits and are ideal for confirming on- and off-target CRISPR gene editing experiments.

Design custom panels for your genome editing research

Our rhAmpSeq Design Tool lets you quickly and easily design custom rhAmpSeq CRISPR Panels specific to your application and targets of interest (Figure 1). If you would like additional assistance, our expert bioinformatics team can help tailor a design for your custom project (Contact us).

Once your design is complete, we provide a detailed summary report of the custom panel results for you to review and, when necessary, iterate your design before you order your custom rhAmpSeq CRISPR Panel. Also available for download are the associated assay BED files and assay IDs to order any sub-panel from the set of assays that were a part of your custom design.

Figure 1. Overview of the rhAmpSeq Design Tool workflow.

Custom rhAmpSeq design

Custom assay design involves two key steps that provide improved performance over other amplicon sequencing systems:

Assay design includes extensive target site review and rhAmp primer design for each target, followed by a comprehensive QC of each rhAmp primer to mitigate off-target effects, such as primer-dimer formation and non-specific genomic hybridization.
Virtual assay pooling is a unique multiplex primer QC feature that further enhances the on-target amplification of rhAmp PCR technology. It allows for more accurate predictions of which potential primer-dimer amplification products could lower overall reaction efficiency and decrease the percentage of correctly mapped reads.

Any assay that is successfully designed but not able to be pooled into the primary panel will be placed in secondary panels. These secondary panels have a designated prefix (such as P2 or SC) in the resulting panel name that correlates to user input during the design submission. Refer to the rhAmpSeq Design Tool User Guide for more information.

Technical details

Custom rhAmpSeq CRISPR Panels are available in three convenient scales to fit your experimental needs: 0.4 nmol, 4 nmol, and 8 nmol. As shown in Table 1, we recommend adjusting rhAmp primer concentrations in the first amplification reaction (Targeted rhAmp PCR 1) depending on your panel size (plexity). Table 1 shows the approximate number of reactions for each scale based on panel size.

Table 1. Number of rhAmp primer reactions based on scale and panel size.

Panel size	rhAmp primer concentration in 10X panel*	Number of reactions per rhAmp primer order	Example
			Panel size	Number of reactions
			Panel size	0.4 nmol primer (x)	4 nmol primer (x)	8 nmol primer (x)
≥500-plex	50 µM total primers	x nmol of primer/(0.1 nmol total/panel size)	1000	4000	40,000	80,000
			750	3000	30,000	60,000
			500	2000	20,000	40,000
101–499-plex	100 nM each primer	x nmol of primer/0.0002 nmol per rxn	400	2000	20,000	40,000
101–499-plex	100 nM each primer	x nmol of primer/0.0002 nmol per rxn	200	2000	20,000	40,000
≤100-plex	250 nM each primer	x nmol of primer/0.0005 nmol per rxn	100	800	8000	16,000
			50	800	8000	16,000
			25	800	8000	16,000

* Important: When creating rhAmpSeq primer pools, do not to combine forward and reverse primers for long-term storage. The primer concentrations in the 10X panel stocks assume there will be a separate forward pool of primers and a separate reverse pool of primers. Refer to the protocol in the Resources section for details.

Product Data

Panel uniformity

High uniformity and on-target amplification with rhAmpSeq CRISPR Panels allow for interrogation of on- and off-target editing in a single library prep with PCR amplification as represented below using the popular AAVS1 “safe harbor” site (Figure 2). All 28 empirically identified off-target sites can be verified when Cas9 is constitutively expressed in HEK293 cells. Using ribonucleoprotein (RNP) delivery of the Cas9/guide complex in conjunction with Alt-R™ S.p. HiFi Cas9 Nuclease V3 dramatically reduces off-target editing.

Figure 2. High uniformity and on-target amplification with rhAmpSeq CRISPR Panels allow for interrogation of on- and off-target editing in a single library prep with PCR amplification. HEK293 cells constitutively expressing S.p. Cas9 nuclease were electroporated with 10 µM AAVS1-targeting Alt-R sgRNA. Alternatively, standard HEK293 cells were electroporated with 4 µM Alt-R wild-type (WT) or HiFi Cas9 Nuclease complexed to the AAVS1 sgRNA (at a 1:1.2 protein to gRNA ratio), including 4 µM Alt-R Cas9 Electroporation Enhancer using the Amaxa™ Nucleofector™ 96-well Shuttle™ System (Lonza) (n = 1 transfection per condition). gDNA was isolated and amplified using a custom rhAmpSeq CRISPR Panel containing amplicons for the on-target and 28 of the top off-target sites identified by GUIDE-Seq. Amplicon sequencing on the Illumina MiSeq™ (v2 chemistry, 150 bp paired-end reads) was performed and analyzed using the rhAmpSeq CRISPR Analysis Tool (n = 1 amplification per condition). (A) The histogram of panel coverage shows 100% of assays have read coverage depth that is >0.2X of the mean read coverage depth for all assays in the panel, indicating highly uniform enrichment via amplification. (B) Fragment analysis of final panels in duplicate shows the expected fragment sizes of 300–400 bp with no primer dimers present. (C) NHEJ editing for the on-target locus (Assay 1) and off-target loci (Assays 1–29) is reported using an untreated control for background subtraction. Background editing was <0.2% for all assays in this panel.

Resources

User guides and protocols

rhAmpSeq CRISPR Analysis Tool user guide (9.8 MB)

rhAmpSeq for CRISPR library preparation protocol (1.3 MB)

rhAmpSeq CRISPR Design Tool user guide (2.8 MB)

Requirements for custom panel design

Input requirements–rhAmpSeq assay designs (295 KB)

Application notes and case studies

Evaluate CRISPR-Cas9 edits quickly and accurately with rhAmpSeq targeted sequencing

Sample data

For more information, refer to the analysis guidelines in the User guides and protocols section.

CRISPR sample data–rhAmpSeq analysis (35.3 MB)

Brochures and flyers

rhAmpSeq CRISPR Analysis System product card (116 KB)

Certificates of analysis (COAs)

Find COAs by batch or lot number

Frequently asked questions

How long is my data retained in the rhAmpSeq CRISPR Analysis Tool?

The rhAmpSeq CRISPR Analysis Tool has retention policies for the following data types:

FASTQ files (input) = 30 days from last use

BED files (input) = 30 days if unpaired OR 5 years after pairing

All results files (output) = 1 year from date of generation

Please make sure these times are kept in mind for downloading/storing copies of results in longevity. It should be noted that there is no way to recover files after a retention period has lapsed. At this point the files will either need to be re-uploaded (inputs) or re-analyzed (outputs) by the end user to be available after the retention period has lapsed.