What Jumpcode Genomics does

Jumpcode Genomics is a privately held life-sciences tools company, founded in 2016 and headquartered in San Diego, California, that develops and sells CRISPR-Cas9 based nucleic-acid depletion reagents branded as DepleteX™ and CRISPRclean™. The company's core technology uses pools of designed guide RNAs to cleave abundant, uninformative sequences — ribosomal RNA, mitochondrial DNA/RNA, globin, high-expressing housekeeping transcripts, and host DNA in microbiome samples — in next-generation sequencing (NGS) libraries prior to sequencing, redistributing read capacity toward biologically relevant molecules. The product portfolio spans core kits (Single Cell RNA Boost, Mitochondrial DNA Depletion, Human DNA Depletion, Stranded Total RNA Prep with rRNA depletion for human/mouse/rat plus 212 bacterial species), add-on panels (Nasopharyngeal Microbial RNA Boost, High Expressing RNA, Globin, Insulin), bulk-format reagents for high-throughput screening, and a Custom Guide RNA Design service. Validated integrations with 10x Genomics, PacBio, BD Rhapsody, Element AVITI, and Parse Evercode platforms position the kits as an upstream depletion step in established single-cell and bulk sequencing workflows.

The company sells primarily through direct sales with quote-based pricing (kit-level price points disclosed at roughly $3,000–$7,680 for catalog SKUs), supplemented by a global distribution network anchored by Revvity and regional partners covering DACH, Japan, Korea, France, and ANZ. Customers span academic and translational research institutions (University of Oxford, University of Verona, Polytechnic University of Marche, TGen) and early commercial users (ImYoo), with no disclosed large-pharma reference accounts. Go-to-market emphasizes scientific publications (Genome Research, Cell Reports Methods, bioRxiv), customer stories, technical webinars, and presence at genomics conferences (PAG, ASHG, ASM Microbe, ABRF). Strategic positioning has expanded beyond research tools into public-health and biodefense applications via the BARDA DRIVe partnership and the €24 million EU4Health grant consortium with Ginkgo Bioworks and TGen.

Jumpcode has raised approximately $23.5 million in total disclosed equity funding, including a $21 million Series B in January 2021 co-led by Baird Capital and Arboretum Ventures with LYZZ Capital. The company operates with 11–50 employees and is led by CEO Yaron Hakak (ex-Illumina, Affymetrix, Arena Pharmaceuticals), CFO Brandon Poe (ex-Illumina, Genome Medical), and Chief Scientist Stanley Nelson (UCLA), with board representation from operating partner Frank Witney (former Affymetrix and Dionex CEO). Revenue is not publicly disclosed, and the company has not announced a Series C or IPO as of 2025.

Name

Jumpcode Genomics

Legal name

Jumpcode Genomics, Inc.

Website

https://jumpcodegenomics.com

Company type

Private

Founded year

2016

Operating status

Operating

Headcount range

11–50 employees

Short description

Jumpcode Genomics develops CRISPR-Cas9 based DepleteX™ and CRISPRclean™ reagent kits that remove uninformative sequences (rRNA, mitochondrial DNA, host DNA) from next-generation sequencing libraries, serving academic, biotech, and public-health researchers globally.

Ownership category

akta.pro rank

Product category

Genomics Sample Preparation Reagents

NAICS

Biological Product (except Diagnostic) Manufacturing (325414), Research and Development in Biotechnology (except Nanobiotechnology) (541714)

SIC

In Vitro & In Vivo Diagnostic Substances (2835)

akta.pro primary industry

CRISPR & Functional Genomics Screening Platforms (pooled/arrayed screens, perturb-seq) (HLAAAIAG)

akta.pro secondary industry

Molecular Biology & Genomics Instruments (PCR/qPCR, Sequencing, Microarrays) (HLAGAIAF)

Keywords

• NGS depletion kits
• CRISPR-Cas9 reagents
• Ribodepletion solutions
• Single cell RNA boost
• Microbiome sequencing tools

Headquarters

HQ city

Carlsbad

HQ country

United States

HQ region

North America

Offices2 records

Markets served

GTM type

B2B

Offering type

Hardware or Manufacturing

Cost components

Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure

Revenue model

1. Research Kits and Reagents: Sale of DepleteX™ and CRISPRclean™ reagent kits for NGS library preparation and depletion. Products include single cell RNA boost kits, ribodepletion kits, mitochondrial DNA depletion kits, human DNA depletion kits, and bulk ribodepletion reagents. Revenue generated through direct sales and distributor network.

Pricing tiers

Go-to-market motion1 record

Distribution channels7 records

Marketing channels6 records

Core offering

Jumpcode Genomics develops and sells CRISPR-Cas9 based nucleic acid depletion kits (branded DepleteX™ and CRISPRclean™) that remove abundant, uninformative sequences — such as ribosomal RNA, mitochondrial DNA, globin transcripts, and high-expressing housekeeping genes — from next-generation sequencing (NGS) libraries prior to sequencing. The portfolio includes single cell RNA boost kits, ribodepletion kits, mitochondrial and human DNA depletion kits, tissue-specific RNA depletion panels, bulk ribodepletion reagents, and custom guide RNA design services for life sciences researchers.

Product overview

Jumpcode Genomics offers a CRISPR-Cas9 based technology platform called DepleteX™ / CRISPRclean™ for removing unwanted sequences from NGS libraries prior to sequencing. The product portfolio consists of: (1) Core depletion kits including DepleteX™ Single Cell RNA Boost Kit (KIT1037), DepleteX™ Mitochondrial DNA Depletion Kit (KIT2002), DepleteX™ Human DNA Depletion Kit (KIT2020), CRISPRclean™ Plus Stranded Total RNA Prep with rRNA Depletion (KIT1016), and CRISPRclean™ Stranded Total RNA Prep with rRNA Depletion (KIT1014); (2) Add-on depletion panels including DepleteX™ Nasopharyngeal Microbial RNA Boost (KIT1039), DepleteX™ High Expressing RNA Depletion Kit (KIT1020), DepleteX™ Globin Depletion Kit (KIT1024), DepleteX™ RNA Depletion Panel/Insulin (KIT1025), and Bulk Ribodepletion Reagents (KIT1026); (3) Custom Guide RNA Design service for customized depletion panels. These products work together as an integrated workflow—core kits provide foundational depletion capabilities while add-on panels offer targeted depletion for specific tissues or applications, all utilizing the patented CRISPR-Cas9 mediated depletion technology to remove abundant uninformative sequences and redistribute sequencing reads to biologically relevant molecules.

Differentiator

Problem solved

Functional benefit

Brands

• DepleteX™: Programmable endonuclease technology platform for NGS depletion using CRISPR-Cas9 to remove uninformative sequences.
• CRISPRclean™

Products and services

• DepleteX™ Single Cell RNA Boost Kit A CRISPR-Cas9 based kit that removes ribosomal, mitochondrial, non-variable gene fragments, and other uninformative reads before single cell RNA sequencing, redistributing ~50% of sequencing clusters to informative reads. Validated for short and long read sequencing with 10x Genomics, PacBio, and BD Rhapsody platforms; 24 samples per kit.
• DepleteX™ Mitochondrial DNA Depletion Kit CRISPR-based depletion kit that removes mitochondrial DNA or RNA from human-derived tissue samples with high mitochondrial content, redirecting sequencing reads to biologically valuable information.
• DepleteX™ Human DNA Depletion Kit CRISPR-based depletion kit that removes human DNA from microbiome samples with high human contamination, achieving a 16-fold increase in bacterial reads and unbiased preservation of microbial community composition.
• CRISPRclean™ Plus Stranded Total RNA Prep with rRNA Depletion Stranded total RNA library prep with integrated ribosomal RNA depletion targeting 200+ bacteria species in addition to human, mouse, and rat rRNA. Achieves >80% depletion of eukaryotic and bacterial rRNA, suitable for complex samples containing mixtures of eukaryotic and bacterial cells; 24 samples per kit.
• CRISPRclean™ Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat) Specific, unbiased rRNA depletion and library prep for RNA-seq targeting human 5S, 5.8S, 18S, 28S, 45S precursor, and mitochondrial rRNA genes; provides >98% strand specificity and high-quality representation of transcripts.
• DepleteX™ Nasopharyngeal Microbial RNA Boost Removes abundant human RNA from nasopharyngeal samples to boost discovery of novel microbes and pathogens; enables pathogen detection at Cq values up to 30 with 4 million reads.
• DepleteX™ Rare Transcript Boost Kit (High Expressing RNA Depletion Kit) Broad RNA depletion panel removing the ~4,450 highest expressing transcripts from poly-A selected RNA-Seq libraries derived from fibroblasts and whole blood, reassigning ~70% of sequencing reads to low-expressing biologically relevant transcripts and providing ~5-fold increased coverage of lower expressing transcripts.
• DepleteX™ Globin Depletion Kit Removes four highly expressed human globin transcripts (HBA1, HBA2, HBB, HBD) from RNA-seq libraries, achieving >99% depletion and redistributing sequencing clusters to biologically relevant transcripts for maximized UMI and gene sensitivity.
• DepleteX™ Insulin Depletion Kit Tissue-specific depletion panel removing highest expressing insulin transcripts from pancreatic tissue samples, reassigning sequencing reads to lower expressing transcripts for increased coverage.
• CRISPRclean™ Bulk Ribodepletion Reagents (Human, Mouse, Rat) High-throughput rRNA depletion reagents for up to 1536 samples (96 samples per reaction pool); designed for DRUG-Seq and high-throughput screening applications with >99% rRNA depletion per sample.
• Custom Guide RNA Design Service Customized CRISPRclean reagent design service for removing unwanted DNA or RNA fragments from NGS libraries; experience with plant genomes (maize, wheat), mammalian genomes, and tissue-specific RNA-seq panels; supports automation-friendly formats.

Quantifiable outcome

• ~50% boost in reads useful for secondary analysis in single cell RNA-seq
• +6 more outcomes

Named customers5 records

Segments4 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration5 records

Feature4 records

Partnerships

Ten partnerships are on record, tiered core and flagship.

• ERS GenomicscoreOEM/ Whitelabel/ Licensing Partner · 27 March 2025Non-exclusive CRISPR/Cas9 license agreement providing Jumpcode access to CRISPR gene editing technology to enhance next-generation sequencing capabilities.
• Ginkgo BioworksflagshipStrategic or Co-development Partner · 1 January 2025Part of Ginkgo Technology Network consortium. Jumpcode contributing depletion technology to €24M EU4Health grant program for developing rapid, point-of-care sequencing-based test for respiratory pathogens.
• Ginkgo Bioworks Technology NetworkcoreGTM or Marketing Partner · 28 February 2024Jumpcode joined Ginkgo's Technology Network as an inaugural partner providing integrated R&D capabilities for biosecurity and cell programming applications.
• 10x GenomicsflagshipTechnology or Integration10x Genomics Compatible Products Partner. Jumpcode Single Cell RNA Boost Kit validated with 10x Genomics Chromium Single Cell 3' and 5' Gene Expression platforms, Visium Spatial, and multiome workflows.
• PacBioflagshipTechnology or IntegrationPacBio Compatible Partner. Combination of Jumpcode Single Cell RNA Boost Kit and PacBio MAS-Seq for 10x Single Cell 3' kit maximizes usable single cell RNA sequencing data.
• Element BiosciencescoreTechnology or IntegrationCollaboration and co-marketing partnership validating Jumpcode's CRISPRclean technology on Element's AVITI System. Demonstrated improved data quality and cost savings across genomic applications.
• BD (Becton, Dickinson and Company)coreTechnology or IntegrationPartnership for BD Rhapsody Whole Transcriptome Analysis integration. DepleteX Mito DNA Depletion Kit compatible with BD Rhapsody WTA workflow for improved single cell data in challenging samples.
• Translational Genomics Research Institute (TGen)flagshipStrategic or Co-development PartnerResearch collaboration for COVID-19 genomic sequencing and pandemic preparedness. Joint publication in Cell Reports Methods demonstrating CRISPR-NGS approach for universal infectious disease testing.
• RevvitycoreChannel Partner/ Reseller/ DistributorGlobal distributor for Jumpcode's range of programmable endonuclease enzymes and ribodepletion solutions.
• Scientific Advisory BoardcoreOthersBoard includes Gene Yeo (UCSD), Shawn Levy (Cellanome), Stan Nelson (UCLA), Nik Schork (HonorHealth), Andrew Su (Scripps). Provides scientific guidance and industry expertise.

Scale indicators4 records

Recent moves7 records

Expansion highlights6 records

Direct peers

• Lexogen: Lexogen offers RiboCop, SIRV, and QuantSeq ribodepletion and library prep kits that compete head-to-head with Jumpcode's CRISPRclean RNA Prep and DepleteX kits in RNA-seq workflows.
• New England Biolabs: New England Biolabs offers NEBNext rRNA Depletion Kits and a broad NGS sample prep portfolio that directly competes with Jumpcode's CRISPRclean and DepleteX kits for ribodepletion and library prep workflows.

Broad incumbents

• QIAGEN: QIAGEN's QIAseq FastSelect rRNA and globin removal kits are direct competitive reagents to Jumpcode's depletion panels, distributed as part of a much broader life sciences tools portfolio.
• Illumina: Illumina's Ribo-Zero Plus and TruSeq ribodepletion products compete with Jumpcode in NGS sample prep, while Illumina's sequencing platforms also serve as upstream/downstream context for Jumpcode's depletion kits.
• PerkinElmer (Revvity): Revvity (formerly PerkinElmer) is both a global distributor of Jumpcode's ribodepletion reagents and a broader competitor in NGS sample prep and diagnostics, illustrating the dual channel/competitive relationship.
• Bio-Rad Laboratories: Bio-Rad offers the SEQuoia Complete Library Prep Kit with ribodepletion for NGS workflows and serves comparable academic and biotech customers, though as part of a much broader life sciences portfolio.
• Integrated DNA Technologies (IDT): IDT offers rRNA depletion and library prep products under the xGen brand and serves overlapping NGS sample prep customers; it also provides custom oligo services that compete with Jumpcode's Custom Guide RNA Design.
• Roche (KAPA Biosystems): Roche's KAPA RNA HyperPrep and ribodepletion reagents are widely adopted NGS sample prep products that compete with Jumpcode in research and clinical sequencing workflows.

Others

• Ginkgo Bioworks: Ginkgo Bioworks is a strategic co-development partner on the €24M EU4Health POC respiratory test and Ginkgo Technology Network member; while not a reagent competitor, it represents both a partnership channel and a benchmark for synthetic biology-driven platform plays.
• 10x Genomics: 10x Genomics is a Compatible Partner that validates Jumpcode's Single Cell RNA Boost Kit on Chromium and Visium platforms, but is also a strategic sequencing platform provider whose roadmap decisions shape Jumpcode's addressable market.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks5 records

Key highlights7 records

Customer concentration

• LinkedInlinkedin.com/company/jumpcodegenomics
• Xtwitter.com/JumpcodeG

Revenue estimate

Valuation estimate

Number of profiles

Profiles17 records

Funding overview

Funding rounds2 records

Investors3 records

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Jumpcode Genomics