Quick Start
CRISPRclean Single Cell

CRISPRclean Single Cell RNA Boost Kit Product Support

The resources below are designed to help you boost your research with Jumpcode. If you have questions, you can reach us at [email protected].

Getting started

Read this before you start your experiment. This PDF download contains a high-level overview of the process, frequently asked questions, and support contact info in case any issues arise during your experiment or analysis.

There are two versions to choose from:

Single Cell with CRISPRclean Depletion

Single Cell with CRISPRclean for PacBio MAS-seq

Analysis guidelines


We have multiple options to support your analysis needs. Choose from:


User manual

Depletion content

Download public data set files


Can I use the CRISPRclean depletion on mouse samples?
Yes, but the depletion rate is lower since the guides were designed for human samples
Does the CRISPRclean depletion use all of the cDNA from my 10X prep?
No, only ΒΌ of the available cDNA from a given 10X prep is used.
Is this kit compatible with the 5’ Chromium assay? What about Visium spatial?
Yes, it is compatible with both kits. Our depletion panel is designed to tile across the full length of transcripts.
What is the sequencing depth recommendation for the depleted condition?
In general, single cell users use between 25K –50K reads/cell depending on their application. For the depleted condition, users can choose to sequence 12.5K –25K reads/cell to see the same information or sequence at the same depth to see more information.
Can I use SPRI beads instead of AMPure beads?
Yes, we have tested this in-house and they both work with our assay.