CRISPRclean Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat) - 24 Samples
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CRISPRclean Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat) - 24 Samples

CRISPRclean Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat) - 24 Samples

JumpcodeSKU: JUM-KIT1014
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Description

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

RNA samples frequently contain up to 90% ribosomal RNA. Transcriptome sequencing without removing these overabundant rRNA sequences reduces sequencing capacity and makes it harder to detect lower expressing, biologically relevant transcripts. See how CRISPRclean can help your research with effective rRNA removal.

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
Specification
Catalog JUM-KIT1014
Samples per kit 24
Assay time 7.5 hours
Hands-on time 3 hours
Sample types Total RNA
Input quantity 5 to 100 ng
Strand specificity >98% Directional and strand specific
Compatible species Human, mouse, and 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. Requires KIT1017 CRISPRclean Unique Dual Index Adapter Plate for RNA Prep (Set A)

 

One-day workflow from RNA to sequencing-ready library

CRISPRclean workflow
CRISPRclean Workflow HMR Timeline

Specific and unbiased

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.

CRISPRclean Depletion

CRISPRclean depletion ERCC controls at 5 ng input

RiboZero Plus Depletion

RiboZero Plus Depletion

Effective single tube, multi-species depletion

>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).

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