Maximized guide detection. Maximized discovery.

Amplify a CRISPR guide sequence derived from a CROP-style vector alongside your standard RNA Sequencing Library.



The ScaleBio CRISPR Guide Enrichment Kit is modified from our standard ScaleBio Single Cell RNA Sequencing Kit, with the added benefit of capturing a CRISPR guide sequence derived from a CROP-style vector.

To maximize guide detection, we have included target-specific priming during reverse transcription, as well as PCR enrichment in the final step of library preparation.

This kit enables the processing of up to 500,000 cells or nuclei per run with extended throughput, as well as the multiplexing of up to 96 samples.


Cell Throughput

125,000 cells or nuclei per run, or up to 500,000 cells or nuclei per run with Extended Throughput Kit

Recommended input

10,000 cells per well (Initial Distribution)

Sample Throughput

Up to 96 samples per run

CRISPR Guide Enrichment Workflow

CRISPR libraries are designed, assembled into lentiviral vectors, which are used to transfect cells with individual guides.

Cells are then fixed according to the ScaleBio Sample Fixation Protocol.  A guide-specific RT primer is included Indexed Reverse Transcription, improving guide detection.  From the final pooled library, a guide enrichment PCR is performed prior to sequencing.

CRISPR Workflow_v2_20Oct23

30% increase in guide detection with ScaleBio's custom RT Primer

Human A375 cells were used to test guide detection using the custom RT primer in our CRISPR Guide Enrichment Kit and then
compared to the use of of only PolyA priming during reverse transcription. The use of a custom RT primer significantly improves guide detection-enabling lower overall sequencing costs.

CRISPR stats graph

Custom Priming substantially increases guide detection rate across cell types

When comparing guide detection rates (≥3 UMIs per guide) using a traditional CROP-seq primer, a higher percentage of guides are detected both at the population level as well as in the percentage of cells with an identified guide with the ScaleBio CRISPR Guide Enrichment Kit.

Traditional PolyA Primer

CROPseq Original

ScaleBio CRISPR Guide Enrichment


Frequently asked questions

We do provide a software tool specific to the CRISPR Guide Enrichment Kit.

We have tested compatibility on MiSeq, iSeq, NextSeq 500/550, NextSeq 1000/2000, NovaSeq6000.

Even with a 10-fold increase in throughput, our combinatorial indexing method results in an effective doublet rate of ~4.7%.


Want to learn more?


Featured publications View All

High content single-cell combinatorial indexing.

Nature Biotechnol. July 2021.


Want to learn more about the Single Cell CRISPR Guide Enrichment Kit?

Reach out to our Team for more information or to request a price quote.

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