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

Identify lower expressing transcripts with CRISPRclean Plus

200+ bacteria species targeted for ribosomal RNA removal 3-7X increase in microbial coverage in NSP samples 1 day workflow

Complex samples may have a mixture of bacterial and human cells, all actively expressing ribosomal RNA. Take advantage of the power of CRISPRclean for effective ribosomal RNA removal. CRISPRclean can also remove uninformative bacterial reads in-vitro ahead of sequencing – redistributing >80% of sequencing reads to enable identification of lower expressing, biologically relevant transcripts.


  • 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

Catalog KIT1016
Samples per kit 24 samples
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
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. Requires KIT1017 CRISPRclean Unique Dual Index Adapter Plate for RNA Prep (Set A)

CRISPRclean Plus Workflow

CRISPRclean workflow


>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.

Increased sequencing reads for microbial organisms 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.

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

24 samples

$3,600 Add to Cart


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For the US patent, the patent number is US 10,604,802 entitled Genome Fractioning. The patent publication is available here.

For the EP patent, the patent number is EP3102722 entitled Genome Fractioning. The patent publication is available here.