CRISPR-based NGS Library Depletion

CRISPR-based NGS Library Depletion

Don’t Waste your Valuable Reads for Repeatedly Captured Sequences

The ability to sequence millions of reads from genomes and transcriptomes has yielded an unprecedented discovery on genes and genetic variation. Unfortunately, much of these reads are wasted on over abundant sequences that are captured repeatedly.

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Future discovery may be accelerated by cutting through the noise of over abundant sequences. Shifting focus away from abundant genes and increasing sensitivity by lowering background noise is required to enable this discovery. It’s why our partner Jumpcode created CRISPRclean.

CRISPRclean® Technology from Jumpcode Genomics harnesses the specificity of CRISPR-Cas9 to degrade abundant, uninformative sequences in next-generation sequencing (NGS) libraries. With CRISPRclean, you can see more lower expressing transcripts and shift your sequencing power for deeper coverage and improved signal.

Now you can see exactly what you want, breaking through the clutter—and breaking new ground. 

How CRISPRclean works


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CRISPRclean mediated depletion can be integrated directly into NGS library prep protocols at various points depending on the application. CRISPR-Cas9 complexes are formed with a pool of designed guide RNAs. After targeted sequences are cut, they cannot be a substrate for PCR amplification or subsequent sequencing. The output is a refined, sequence ready NGS library. 

Benefits

  • Highly programmable
  • Increased sensitivity
  • Simple automatable workflow
  • Genomic analysis platform agnostic

Applications

CRISPRclean technology is both specific and highly programmable to remove unwanted sequences for many applications. View the applications below to learn how Jumpcode is driving discovery today.

Whole Transcriptome Profiling 

~90% of total RNA is abundant ribosomal RNA noise. This high abundance of ribosomal sequences in samples often results in more background noise than usable data. Detecting novel transcripts or low-expressing transcripts becomes a time-consuming challenge, where the biologically relevant data you need is often lost in the clutter. With CRISPRclean Ribodepletion Kits, you can access an unbiased whole transcriptome – without the noise.

Single Cell Analysis 

Boost usable single cell RNA seq data and gain a deeper view of expression profiles of individual cells with the CRISPRclean Single Cell RNA Boost Kits for human or mouse. The Kits deplete sequences not used for secondary analysis including unaligned reads, ribosomal, mitochondrial, and non-variable genes

Microbiome

Improve microbial genome coverage and increase detection sensitivity of low abundant microbial species with CRISPRclean. With the CRISPRclean Human DNA Depletion Kit (coming soon) or the CRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion Kit you can gain an accurate taxonomic profile of a microbial community by removing human host DNA or RNA. 

Infectious Disease Surveillance 

Detect known and novel pathogens to accelerate outbreak investigations. You can acquire viral genomic data, microbiome composition, information on co-infections, and host-immune response in a single workflow with the CRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion. Please refer to the Application Note CRISPRclean® Plus for SARS-CoV-2 Shotgun Metatranscriptomic Sequencing for further information.

Custom depletion panels for your samples and applications are available upon request, please contact us if you are interested.

CRISPRclean Depletion Panels

In addition to the library preparation kits we also offer Jumpcode's CRISPRclean Depletion Panels with different focused panels for increasing detection sensitivity of low expressing transcripts and one broad RNA depletion panel to maximize low expressing transcripts.