Applications & more

Discover more about our applications in the Samplix Knowledge Center, which includes webinars, scientific posters, and research papers.

Create the ideal home for functional analyses of cells

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What could you achieve if you boosted the speed and accuracy of your functional analyses of living cells?

Xdrop and Xdrop Sort change how you analyze cells by transforming bulk functional analyses and bulk screening into rapid and accurate assays with a unique single-cell format.

Pictured: Co-encapsulated lymphoblasts and natural killer cells with staining to show the successful immune reaction. Top left: bright field image; top right: CFSE staining for natural killer cell; bottom right: eFluor670 staining for lymphoblast; bottom left: PI staining to show dead cell.


Validating gene edits and more

Validating CRISPR edits and identifying CAR cassette insertions are essential to cell and gene therapy research. Xdrop and Xdrop Sort have protocols that support highly targeted long-read and short-read sequencing of DNA. The workflow involves encapsulating DNA for targeted enrichment in double-emulsion droplets, then sorting to capture the region of interest. Downstream sequencing reveals unintended on-target and off-target rearrangements that other methods cannot easily find.

Application notes

Featured application for functional analysis of cells:
Rapidly identifying active killer cells

From encapsulation of natural killer (NK) cells and their targets in double-emulsion droplets to successful single-cell, multi-parameter, high-resolution flow cytometry, the workflow in this application note supports fast identification and quantification of the active NK cells.

In this collaboration with Agilent Technologies, we looked at the potential to rapidly identify active NK cells in a cell population. We used our Xdrop droplet-based format for an assay on the Agilent NovoCyte Quanteon flow cytometer. Target cell killing was seen within an hour of incubation, allowing the identification of the fastest killers. The assay is fast as the picoliter droplet volume leads to rapid cell–cell interactions, marking a significant advancement in the study and analysis of immune cells.

Applications for functional analysis of cells

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Rapidly identifying active natural killer cells

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Efficiently finding rare active enzyme variants

IFN γ Cytokine

Revealing highly potent secretors of IFN-γ

multiple chemokine serection

Single cell assay to quantify IFN-γ and TNF-α secretion

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Identifying highly potent TNF-α-secreting T cells from a blood sample

Genomics applications

Samplix AppNote Transgene Insert Analysis 2023 EMR

Simplifying transgene insertion analysis with Xdrop® Sort

Samplix Xdrop App Note Verifying CRISPR chr printed version

Verifying CRISPR edits with Xdrop®

DEtecting HOV18 intergation sites in the human genome using Xdrop

Detecting HPV18 integration sites using Xdrop®


Resolving repetitive and GC-rich regions with Xdrop®

Samplix CYP2D6 pseudogenes AppNote v1.0

Genes vs. pseudogenes

Plant genomics applications

Revealing gene cluster

Revealing the structure of a biosynthetic gene cluster


Gap closing in a plant gene cluster

Technical notes

Featured technical note for genomics:
Duplex Xdrop enrichment

To better elucidate the steps of the Xdrop workflow and how these are connected, we enriched DNA to sequence a well-known gene and highlight the outcome expectations at various milestones from sample preparation to read mapping.

BRCA2 is a human tumor suppressor gene located on chromosome 13. The protein it codes for is responsible for DNA repair. BRCA2 is involved in preventing genomic rearrangements that can be oncogenic, and many of the mutations identified to date in this gene correlate with increased risk of cancer.

Xdrop technical notes

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Encapsulating yeast cells for screening and recovery

Samplix Xdrop TechNote Improved WGA Jan 2022

Improved whole genome amplification with Xdrop

BRCA2 Milestones Tech note V1.0

Enrichment of long DNA fragments for DeepSeq

2007 Samplix technote benchmarking v1.0

Benchmarking Xdrop


Talk from the Natural Killer Cell Symposium 2023

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Achieving single-cell resolution for cytokine secretion and cell-killing assays with Xdrop

In this talk, Dr. Peter Mouritzen discusses how double-emulsion droplet-based technology is changing the approach to cytokine secretion and cell-killing assays by changing the focus from bulk to true single-cell views. He shares the results of assays done in Xdrop double-emulsion droplets as well as describing the technology.

Applied Synthetic Biology in Europe VI (ASBE VI) webinar

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From bulk to single-cell formats: Xdrop changes how we work with yeast

In this video, Jinglin Wang of the SBTY Group at DTU discusses how using mono disperse double-emulsion (DE) droplets generated with Xdrop allow the encapsulation of living yeast cells, supporting single-cell format analyses of yeast as well as sorting to obtain the cells with the desired activity or properties.

Oxford Global Conferences webinar

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Building on a New Approach to Validate Gene Editing and Localize CAR Cassettes in T Cells

Safety and efficacy are key considerations in engineered cell therapies. However, conventional PCR screening for editing outcomes can overlook unintended cassette insertions. Here, Dr. Peter Mouritzen discusses an Xdrop workflow that is proven to overcome this limitation to identify the precise localization of the CAR insertion. The workflow also has applications in validating gene editing.

European Society of Human Genetics 2022

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Target: Rare Disease Insights

At ESHG 2022 in Vienna, Samplix hosted a special event where three experts talked about our novel technology that supports important research into the genetics of rare diseases.

Dr. Peter Mouritzen (Samplix): Xdrop: Targeting Rare Disease Genomics

Professor Alexander Hoischen (Radboud University Medical Center): Indirect targeted accurate long-read sequencing for rare diseases

Professor Sarah Cumming (Institute of Molecular Cell & Systems Biology, University of Glasgow): Xdrop technology can capture genomic DNA fragments that carry the myotonic dystrophy type 1 mutation

SLAS Europe 2022

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Achieving single-cell resolution for cytokine and cell-killing assays with Xdrop

Our CTO and co-founder, Dr. Marie Mikkelsen, describes how the microfluidics technology in Xdrop helps achieve single-cell resolution in important assays for immunotherapy research, such as cytokine secretion and killer cell activity assays. She also talks about why this single-cell resolution is so important.

Festival of Genomics & Biodata 2022

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Mapping and characterization of mouse transgenes using Xdrop technology

Hear how Dr. Lydia Teboul (Head of Molecular and Cellular Biology at the Mary Lyon Centre, MRC Harwell) and her team use the Xdrop target enrichment workflow to map and characterize mouse transgenes.

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How microfluidics is revolutionizing cell and DNA preparation

Our co-founder and CTO, Dr. Marie Just Mikkelsen, gives a talk on the role of microfluidics technology in boosting the throughput and resolution of gene and cell screening. Instruments such as Xdrop and Xdrop Sort are revolutionizing DNA and cell preparation for downstream analyses by enabling processes such as targeted DNA enrichment for sequencing, single-cell phenotyping, and single-cell assessments of enzyme activity.

NextGenOmics UK 2021

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Functional validation of multiomics data – CRISPR perks and nuisances

Dr. Claudia Kutter, Karolinska institute, talks about how her lab uses CRISPR editing to elucidate the role of non-coding RNAs in transcriptional regulation. She tells about how the lab optimized CRISPR editing to modify cell lines but discovered unintended genomic rearrangements that were otherwise unidentified by traditional methods. Here she shows how they were able to identify unintended edits by using Xdrop targeted enrichment combined with long-read sequencing

ESHG 2021 – Samplix Corporate Session

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Long-read whole genome analysis of single human cells

Talk by DR. ADAM AMEUR, Uppsala University and Science for Life Laboratory (SciLifeLab), at ESHG 2021 Virtual.

Leveraging the unbiased droplet multiple displacement amplification (dMDA) step of Xdrop®, Dr. Ameur prepared long fragments of gDNA from a single cell for HiFi PacBio sequencing. 2.5 million reads per cell and up to 40% genome coverage revealed comparable numbers of SNV as seen with short-read sequencing, but four times as many structural variants. The method presented goes far beyond limits of current long-read sequencing protocols, which normally require at least 5 ng of input DNA.

Samplix Webinar – Pitfalls and best practices for CRISPR/Cas9-based gene editing


Another two-part webinar featuring a collaboration with Bioneer. Benjamin gives specific recommendations for planning a successful gene editing strategy in "Ten things you should think of when designing a good gene editing strategy". Then, Peter provides advice for subsequent validation of your edits in "How to ensure your gene editing validation accounts for larger unintended rearrangements."

Samplix Webinar – Certainty After CRISPR

PAUL ERIC BENNETT, COBO Technologies, and KEYI GENG, Karolinska Institute.

A two-part webinar discussing unanticipated alterations happening after gene editing and ways to detect and characterize expected and unexpected outcomes. In "Fast and sensitive detection of indels induced by precise gene targeting", Paul surveys the pros and cons of current InDel detection methods and how to choose the one that is fit for purpose. Keyi describes her detective work in uncovering and fully characterizing unexpected outcomes of a gene editing strategy in "Where did the target region go? Unravelling odd CRISPR/Cas9-induced genomic alterations in human cells."

Genome Editing Oxford 2021 Virtual

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Validation of Genome Editing Through Indirect Sequence Capture and Long-Read Sequencing

Talk by PETER MOURITZEN, Vice President Application and Market Development, Samplix, at Genome Editing 2021 Virtual.

• Methods commonly used to validate genome editing may fail to detect unintended modifications occuring during editing with considerable ramifications for results.
• By enriching long DNA fragments over and around the region of interest, the Xdrop® indirect sequence capture provided by Samplix® offers a novel high-resolution alternative validation.
• Show case: Xdrop-based validation reveals an unwanted alteration in an engineered human cell line.

Festival of Genomics 2021

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Identification of functional proteins densely co-encoded in the human genome

Talk by ALEX KHITUN, Postdoctoral Researcher at Harvard Medical School

  •  Description of small open reading frame (ORF)-encoded proteins
  •  Discovery via buttom-up proteomics of small ORF-encoded proteins overlapping RPL36
  •  Assessment of structure and function of these densely encoded proteins
  •  Validation of knockout cell lines using Xdrop®
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CRISPR validation and resolving complex genomics landscapes with Xdrop

Talk by PETER MOURITZEN, VP Application & Market Development at Samplix

  •  Indirect Sequence Capture of any genomic region: the Xdrop® microfluidics system
  • Validation of CRISPR edited cell lines detecting unintended kb-long insertions
  • Identification of integration sites and structural variation in transgenic mice
  • Reconstruction of complex genomic regions: CYP2D6 gene without confounding effects of pseudogenes
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Genomically humanized mouse models of neurodegenerative disease

Talk by TOM CUNNINGHAM, Senior Investigator Scientist at MRC Harwell

  • Engineering and studying a new generation of knock-in mouse models of motor neuron disease and frontal temporal dementia
  • Genomic humanisation refers to replacement of entire mouse genes with the human orthologous sequence
  • Allele QC is critical in order to accurately study the consequences of pathogenic mutations

NextGen Omics Nov 2020 Virtual

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Tackling Disease Related Repeat- Expansion Analysis By Xdrop® Indirect Sequence Capture

Talk by MARZIA ROSSATO, Researcher in Genetics, University of Verona, at the NextGen Omics conference 2020.

• The analysis of long DNA fragments provides consistent benefits in the characterization of clinically-relevant regions with challenging features, such as tandem repeats, structural variants, and high CG-content
• The Xdrop indirect sequence capture provided by Samplix® represents a flexible approach to enrich for long DNA fragments of interest and sequence them using either short or long reads
• Show case: Xdrop can be efficiently applied for the analysis of SNV, tandem repeat length and interruption in genes underlying neurological disorders

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Xdrop – Validation Of Correct CRISPR Gene Editing

Talk by PETER MOURITZEN, Vice President Application and Market Development, Samplix, at NextGen Omics conference 2020

The Xdrop concept of Indirect Sequence Capture allows on-target analysis of 40 kb or more of the genomic region surrounding gene editing sites
• Case study: Detection of unintended on-target editing in a set of IPS cell lines
• Additional strategies for targeted enrichment to analyse for CRISPR on- and off- target events, CRISPR knock-in and other transgene integration patterns

Samplix Webinar June 2020

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Samplix Webinar: Capture the dark genome: From repeat-expansions to CRISPR unintended mutations

PART 1 (01:30): Tackling Disease-Related Repeat-Expansion Analysis - Dr. Marzia Rossato, Researcher, Functional Genomic Lab, University of Verona, Italy

PART 2 (20:44): Validation of CRISPR in a 100 kb Region Surrounding the Editing Site - Dr. Peter Mouritzen, Application Development Services, Samplix, Denmark

PART 3 (37:50): The Launch of a Grant Program and Q&A

Scientific papers

Click on a headline to open up more info about scientific papers.



Long-read whole genome analysis of human single cells

Hård, J., Mold, J.E., Eisfeldt, J. et al.

Nat Commun 14, 5164 (2023). DOI:


Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation for X-linked genes

Giovenino, C., Trajkova, S., Pavinato, L. et al. 

Eur J Hum Genet (2023). DOI: 



Population-wide gene disruption in the murine lung epithelium via AAV-mediated delivery of CRISPR-Cas9 components

Honglin ChenSteffen DurinckHetal PatelOded ForemanKathryn MeshJeffrey EasthamRoger CaothienRobert J NewmanMerone Roose-GirmaSpyros DarmanisSoren WarmingAnnalisa LattanziYuxin LiangBenjamin Haley

Mol. Ther. Methods Clin. Dev. (2022). DOI10.1016/j.omtm.2022.10.016.


Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells

Keyi GengLara G MerinoLinda WedemannAniek MartensMałgorzata SobotaYerma P SanchezJonas Nørskov SøndergaardRobert J WhiteClaudia Kutter

Genome Res. 2022. 32(10): 1876–1891; DOI: 10.1101/gr.276901.122



Characterization of FMR1 repeat expansion and intragenic variants by indirect sequence capture

Valentina Grosso, Luca Marcolungo, Simone Maestri, Massimiliano Alfano, Denise Lavezzari, Barbara Iadarola, Alessandro Salviati, Barbara Mariotti, Annalisa Botta, Maria Rosaria D'Apice, Giuseppe Novelli, Massimo Delledonne, Marzia Rossato

Front. Genet. 2021. 12: 743230; DOIi: 10.3389/fgene.2021.743230


Generation and analysis of innovative genomically humanized knockin SOD1, TARDBP (TDP-43), and FUS mouse models

Anny Devoy, Georgia Price, Francesca De Giorgio, Rosie Bunton-Stasyshyn, David Thompson, Samanta Gasco, et al.

iScience. 2021. 24(12): 103463; DOI: 10.1016/j.isci.2021.103463


CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells

Keyi Geng, Lara Garcia Merino, Linda Wedemann, Aniek Martens, Malgorzata Sobota, Jonas Norskov Sondergaard, Robert J. White, Claudia Kutter

bioRxiv 2021.07.01.450727; DOI:


Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24

Xiongwen Cao, Alexandra Khitun, Yang Luo, Zhenkun Na, Thitima Phoodokmai, Khomkrit Sappakhaw, Elizabeth Olatunji, Chayasith Uttamapinant, Sarah A. Slavoff. 

Nat Commun 12, 508, 2021. DOI: 10.1038/s41467-020-20841-6


Verification of CRISPR editing and finding transgenic inserts by Xdrop Indirect sequence capture followed by short- and long- read sequencing

Blondal Thorarinn, Gamba Cristina, Jagd Lea Møller, Su Ling, Demirov Dimiter, Guo Shuang, Camille M. Johnston, Eva M. Riising, Wu Xiaolin, Marie J. Mikkelsen, Szabova Ludmila, Mouritzen Peter

Methods. 2021 Jul;191:68-77. DOI: 10.1016/j.ymeth.2021.02.003.



Reconstruction of the birth of a male sex chromosome present in Atlantic herring

Rafati N, Chen J, Herpin A, Pettersson ME, Han F, Feng C, Wallerman O, Rubin CJ, Péron S, Cocco A, Larsson M, Trötschel C, Poetsch A, Korsching K, Bönigk W, Körschen HG, Berg F, Folkvord A, Kaupp UB, Schartl M, Andersson L.

Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24359-24368. DOI: 10.1073/pnas.2009925117


Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting

Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ.

Hum Mutat. 2020 Sep;41(9):1671-1679. DOI: 10.1002/humu.24063.



Corrigendum to "Generation of a set of isogenic, gene-edited iPSC lines homozygous for all main APOE variants and an APOE knock-out line" [Stem Cell Res. 34/1873-5061 (2019) 101349-55]

Schmid B, Prehn KR, Nimsanor N, Garcia BIA, Poulsen U, Jørring I, Rasmussen MA, Clausen C, Mau-Holzmann UA, Ramakrishna S, Muddashetty R, Steeg R, Bruce K, Mackintosh P, Ebneth A, Holst B, Cabrera-Socorro A.

Stem Cell Res. 2020 Sep 21;48:102005. doi: 10.1016/j.scr.2020.102005. Epub ahead of print. Erratum for: Stem Cell Res. 2019 Jan;34:101349. PMID: 32971461.


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Identifying and isolating single immune cells based on their function

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Supporting engineered cell therapy: targeted and accurate assessments of gene editing outcomes

Poster Single molecule amplification

Unbiased Amplification of Single Molecules enables even coverage of chromosomal DNA

long range information poster

Microfluidics based, long fragment, targeted enrichment


Targeted enrichment of long DNA-molecules by droplet sorting for phasing mutation in TP53