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

RNA samples frequently contain up to 90% ribosomal RNA. Transcriptome sequencing without removing these noisy rRNA sequences reduces sequencing capacity and makes it harder to detect lower expressing, biologically relevant transcripts.

CRISPRcleanTM Stranded Total RNA Prep with rRNA Depletion Kit

Specific, unbiased depletion and library prep for RNA-Seq.

Highlights

  • Effective single tube, multi-species depletion with CRISPR-Cas9 mediated technology

  • Increases sensitivity to detect lower expressing, biologically relevant transcripts

  • Optimized library prep and depletion workflow generates high quality representation of transcripts 

  • Consistent full-length, uniform transcript coverage, and high library complexity 

  • One day workflow: 7.5 hours assay with 3 hours of hands-on time

One-day workflow from RNA to sequencing-ready library

CRISPRclean workflow
CRISPRclean Workflow HMR Timeline

CRISPRclean Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat) is a simple and streamlined 1-day workflow from total RNA to sequencing-ready, strand-specific libraries in 7 steps with multiple safe stopping points.

Specific and unbiased

CRISPRclean Depletion

CRISPRclean depletion ERCC controls at 5 ng input

RiboZero Plus Depletion

RiboZero Plus Depletion

CRISPRclean Stranded Total RNA Prep with rRNA Depletion produces extremely low library bias. ERCC reads counts were highly correlated, between depleted (y-axis) and undepleted libraries (x-axis), indicating the CRISPRclean rRNA depletion method is highly specific, unbiased, and accurate. This allows for gene expression measurements to be more accurately represented than those that would be obtained from an undepleted sample. Illumina RiboZero Plus Depletion paired with Jumpcode’s stranded RNA prep shows lower ERCC read count correlation and higher bias.

Performance

Effective single tube, multi-species depletion

>90% rRNA Depletion Across Mammalian Species

>90% rRNA depletion across mammalian species. Universal reference RNAs (Human, mouse, rat, chicken, cow, and dog) were used to assess performance of the ribodepletion across multiple species. 

Optimized library prep and depletion workflow

High reproducibility of read counts

High reproducibility of read counts in replicate CRISPRclean libraries. Sequence read counts of ERCC control spiked into 5 ng of UHR RNA input displayed high correlation between depleted library replicates.

High quality representation of human gene expression

(Left) Highly correlated human gene expression between 5 ng and 100 ng UHR RNA inputs. Highly correlated expression means the CRISPRclean workflow is very specific for ribosomal RNA removal and robust regardless of input amount.

(Right) CRISPRclean showed minimal difference in human gene expression levels at 5 ng and 100 ng UHR RNA inputs. Gene level counts were plotted on a Log2 scale (y-axis) and sorted from low to high expression in the 5 ng library. Minimal deviation is seen from a Log2 fold change of 0 which represented highly correlated human gene expression measurements across a range of RNA inputs.

Consistent full-length, uniform transcript coverage

Normalized transcript position

CRISPRclean libraries provide uniform coverage across the length of transcripts. Transcript position is analyzed across genes detected with > 10 reads in CRISPRclean libraries were prepared from 3 replicates of each 5 ng, 25 ng and 100 ng of UHR RNA input.

Increases sensitivity to detect lower-expressing, biologically relevant transcripts

Gene detection at 10x coverage in depleted libraries

The number of genes is assessed at 10x coverage in libraries prepared with different input amounts of UHR RNA. Gene detection is measured by the number of genes detected at 32M subsampled paired-end reads pass filter (PF).

Product ordering

KIT1014 CRISPRclean Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat) for 24 samples

Application Whole-transcriptome sequencing
Assay time 7.5 hours
Hands-on time 3 hours
Sample types Total RNA
Input quantity 5 to 100 ng
Depletion mechanism CRISPR-Cas9 mediated
Strand specificity >98% Directional and strand specific
Compatible species Human, mouse, or rat
Designed to deplete Human 5S, 5.8S, 18S and 28S rRNA genes, 45S rRNA precursor, mitochondrial 12S and 16S rRNA genes
Multiplex Up to 96 unique dual index adapter barcodes

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