CRISPRclean Metatranscriptomics rRNA Depletion Kit

Complex samples may have a mixture of bacterial and human cells, all actively expressing ribosomal RNA. Depletion of both bacterial and human rRNA sequences facilitates identification of lower expressing, biologically relevant transcripts. 

CRISPRclean Metatranscriptomics rRNA Depletion kit

Designed for Illumina NGS libraries the CRISPRclean Metatranscriptomics rRNA Depletion kit includes guide RNAs designed to deplete rRNA from human and over 200 bacterial species in a single workflow. Ideal for human microbiome studies enabling improved sensitivity and performance.


  • Designed to target human and over 200 bacterial species in a single depletion workflow.
  • Access low total RNA inputs below 1 ng previously not possible with pre-library depletion methods.
  • Save time and streamline your workflow by pooling multiple samples in a single depletion reaction post-library preparation.
Species Human, over 200 bacteria
Designed to deplete Human: 5S, 5.8S, 18S, 28S, 45S (precursor), mito 12S, and 16S rRNA; Bacteria: 5S, 16S, and 23S rRNA
Recommended library prep NEB Next Ultra II Directional RNA Library Prep for Illumina
CRISPRclean workflow graphic

CRISPR-powered universal infectious disease assay.

The COVID-19 pandemic has brought intense awareness to the dangers of zoonotic diseases and the real danger they pose to global human health and welfare.

We present an RNA metagenomic NGS protocol using Jumpcode's CRISPRclean technology, that enables detection of the SARS-CoV-2 genome sequence, the source of any co-infection, and the host transcriptional response in a single workflow

Evaluation is based on contrived samples with lung-derived total RNA combined with Staphylococcus aureus total RNA and a synthetic SARS-CoV-2 control. Also two semi-contrived samples from patient stool samples spiked with 600 or 60 copies of the synthetic SARS-CoV-2 control.


  • In contrived samples, CRISPRclean depletion results in a 10-fold increase of reads that map to the SARS-CoV-2 genome and the control S. aureus.
  • In semi-contrived samples, CRISPRclean depletion shows a 4-fold increase in bacterial species detection.
  • SARS-CoV-2 was detectable by sequencing even when present at only 60 copies in the sample.
Fig2_fold enrichment

Product ordering

Each CRISPRclean Metatranscriptomics rRNA Depletion Kit contains enough material for up to 3 reactions, and each reaction can contain up to 16 multiplexed samples.

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