CRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria) 

Complex samples may have a mixture of bacterial and human cells, all actively expressing ribosomal RNA. CRISPRclean™ Plus depletes over 200 bacteria species and human rRNA sequences to enable identification of lower expressing, biologically relevant transcripts.

CRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion Kit

CRISPR-based ribodepletion strategy optimized with stranded RNA prep increases coverage of lower-expressing transcripts from complex biological samples.


  • Streamlined CRISPRclean workflow: stranded total RNA library prep with ribodepletion 

  • Ideal for analysis of samples containing complex mixtures of eukaryotic and bacterial rRNA

  • 3 to 7-fold increase in coverage of SARS-CoV-2 and other genomes in nasopharyngeal (NSP) samples 

  • Single workflow to detect viral genomic data, microbiome composition, co-infections, and host gene expression

CRISPRclean Plus Workflow

CRISPRclean workflow

CRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria) is a streamlined workflow from total RNA to sequencing-ready, strand-specific libraries in 7 steps with multiple safe stopping points.


>80% depletion of eukaryotic and bacterial rRNA in clinical NSP samples

percent ribosomal species mock and depleted

Before and after depletion comparison showed efficient >80% rRNA depletion of eukaryotic and bacterial using clinical NSP samples across different Ct values from negative to 38.93, which has very low viral load.

Top 10 high abundance organisms fold change after depletion

read counts top 10-organisms sample 404

Top ten high abundance organisms in depleted sample S8 (Ct value 26.94). High abundant organisms on average increased 10-fold reads per million compared to undepleted samples.

More gene counts in human gene expression

genes counted in human gene expression for depleted compared to undepleted

Gene expression signals before and after depletion are highly correlated with linearity R2 at 0.8589. R2 close to 1.0 shows that human gene expression is conserved between undepleted and depleted sample S7. Note that there are more gene counts for the depleted sample compared to the undepleted sample.

Increased human gene detection sensitivity

human genes detected in NSP samples after depletion

More genes were detected after depletion compared to undepleted samples. Read count cutoff of 80 was used as CPM of 1.

Increased bacterial detection sensitivity

increased bacterial detection sensitivity with clinical NSP samples

More bacterial species are detected when samples are depleted with CRISPRclean.

Product ordering

KIT1016 CRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria) for preparing 24 samples

Application Infectious disease surveillance
Assay time 9 hours
Hands-on time 3.5 hours
Sample types Complex samples with mixtures of eukaryotes and prokaryotes including nasopharyngeal, saliva, gut, skin, and fecal.
Input quantity 5ng - 100ng
Depletion mechanism CRISPR-Cas9 mediated
Strand specificity >98% directional and strand specific
Compatible species Human, mouse, rat, 212 bacteria
Designed to deplete Human 5S, 5.8S, 18S and 28S, 45S rRNA precursor, mitochondrial 12S and 16S rRNA genes. 212 bacteria representing all phyla: 5S, 16S, and 23S rRNA gene.
Multiplex Up to 96 unique dual index adapter barcodes

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