CRISPR DEPLETION ENABLES SENSITIVE IDENTIFICATION OF VIRAL & BACTERIAL POPULATIONS IN COMPLEX SAMPLES
CRISPRclean® Plus Stranded Total RNA Prep with rRNA Depletion
- 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
- Streamlined Jumpcode® CRISPRclean® workflow: stranded total RNA library prep with ribodepletion
- Automated on the Sciclone® G3 NGSx iQ™ liquid handler
Jumpcode Genomics’ CRISPRclean® Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria) kit is an optimized directional RNA library prep leveraging a CRISPR-powered depletion workflow that increases sensitivity to detect lower expressing and biologically relevant transcripts from complex samples. An optimized workflow with 9-hour total assay time and 3.5 hours of hands-on time (HOT) is made up of 7 simple steps with multiple safe stopping points.
Powered by CRISPR-Cas9, ribodepletion is highly efficient and programmed to cut ribosomal RNA from human sequences (5S, 5.8S, 18S, 28S, 45S (precursor), mitochondrial 12S and 16S sequences), and 212 bacterial species from all phyla (5S, 16S, and 23S rRNA sequences).
Improve your discovery of high-value and biologically interesting transcripts with Jumpcode Genomics’ CRISPRclean® Plus technology.
Fully Automated Protocol
A tested method is available to automate Jumpcode Genomics’ CRISPRclean® Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria) kit on the PerkinElmer Sciclone® G3 NGSx iQ™ liquid handler.
For more information contact [email protected].
Multiplexing with UDI Barcodes for Illumina® Platforms
Up to 1,536 barcodes unique dual index (UDI) barcodes are available for multiplexing CRISPRclean® Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria) libraries.
- NEXTFLEX® RNA-seq 2.0 Unique Dual Index Barcodes (1-384)
This set of 384 UDI barcodes is provided at a concentration optimized for use with Jumpcode Genomics’ CRISPRclean® Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria) kit - NEXTFLEX® RNA-seq 2.0 UDI Barcodes (1 – 1,536) for Ultra-High-throughput RNA-seq Applications
With a set of 1,536 barcodes with UDIs, users can multiplex anywhere between two to 1,536 RNA-seq libraries in a single sequencing run.
| Assay Time | 9 hours |
| Application | Infectious disease surveillance |
| 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 | 5 – 100 ng total RNA |
| Depletion Technology | CRISPR-Cas9 mediated |
| Strand Compatibility | > 98% directional and strand specific |
| Compatible Species | Human, mouse, rat, and 212 bacterial species |
| Designed to deplete | Human 5S, 5.8S, 18S and 28S, 45S rRNA precursor, mitochondrial 12S and 16S rRNA genes, 212 bacterial species representing all phyla: 5S, 16S, and 23S rRNA genes. |
| Multiplex | Up to 1536 UDI adapter barcodes |
For the US patent, the patent number is US 10,604,802 entitled Genome Fractioning. The patent publication is available at https://patentimages.storage.googleapis.com/22/2a/ef/6657ca336c9c08/US10604802.pdf
For the EP patent, the patent number is EP3102722 entitled Genome Fractioning. The patent publication is available at https://patentimages.storage.googleapis.com/a7/54/96/52ed494ab92016/EP3102722B1.pdf
KIT CONTENTS
- CRISPRclean Fragmentation Buffer Mix
- CRISPRclean First Strand Synthesis Mix
- CRISPRclean Reverse Transcriptase
- CRISPRclean Second Strand Synthesis Mix
- CRISPRclean Adenylation Mix
- CRISPRclean Adenylation Enzyme
- CRISPRclean Ligase Mix
- CRISPRclean Ligase Enzyme
- CRISPRclean Cas9
- CRISPRclean 10X Cas9 Buffer
- CRISPRclean RNase Inhibitor
- CRISPRclean PCR Master Mix
- CRISPRclean PCR Primer Mix
- CRISPRclean Nuclease-free Water
- CRISPRclean Resuspension Buffer
Guide RNA box
- CRISPRclean Guide RNA (Human, Mouse, Rat) for rRNA Depletion
- CRISPRclean Guide RNA (Pan Bacteria) for rRNA Depletion
Kit includes stranded total RNA library prep and depletion reagents for 24 RNA-Seq libraries. AMPure® XP beads (Beckman Coulter) and NEXTFLEX® RNA-seq 2.0 UDI barcode barcoded adapters are sold separately and required for this protocol.