Knowledge Center

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

Application notes

Featured application for functional analysis of cells:
Revealing highly potent IFN-γ secretors

Bulk functional assays of mammalian cells can only deliver average readouts for the heterogeneous population, masking the view of individual cell activity. This is due to the cross-talk between cells with different activities in the bulk solution.

The Xdrop double-emulsion droplet workflows described in this application note enable the identification of highly potent IFN-γ-secreting NK-92 cells. This is a unique approach for cytokine secretion assays, delivering single-cell results for living cells within a short time frame.

Featured genomics application:
Revealing CAR cassette insertion sites in T cells

Xdrop facilitates the localization of lentiviral transduction-inserted CAR cassettes in T cells and can help to increase the understanding of edits introduced via viral integrations.

Starting from just 10 ng of DNA, Xdrop reveals gene cassettes inserted using lentiviral and other transductions systems. Around 1,000 unique insertions sites of the CAR cassette inserted all over the genome were revealed using Xdrop in one study. Read the application note to learn more.  

Applications for functional analysis of cells

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Quantifying active killer cells with Xdrop

IFN y assay in droplets application note

Revealing highly potent secretors of the cytokine IFN-γ

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Quantifying immune cells secreting IFN-γ, TNF-α, or both cytokines in one assay

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

Genomics applications

Samplix Xdrop App Note Verifying CRISPR chr printed version

Verifying CRISPR edits with Xdrop®

Samplix TransgeneIntegration AppNote FINAL V2

Finding transgene insertion sites

20220124 AppNoteVirus v2

Detecting viral integrations

Samplix CYP2D6 pseudogenes AppNote v1.0

Genes vs. pseudogenes

EBV App note v2

Unknown regions

Plant genomics applications

Samplix Xdrop App Note Barley biosynthetic gene cluster structure Jan 2022

Revealing the structure of a biosynthetic gene cluster

Samplix Xdrop App Note Tomato gap closing in a gene cluster Jan 2022

Gap closing in a plant gene cluster

Webinars

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

BENJAMIN SCHMID, Bioneer, and PETER MOURITZEN, Samplix

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

Technology

Xdrop uses advanced, proprietary microfluidics technology to generate highly stable double-emulsion and single-emulsion droplets for encapsulating biological material. This versatile and user-friendly instrument safely and rapidly delivers single molecules, nucleic acid fragments, organelles or single cells for a range of high-resolution downstream analyses.

Xdrop Sort builds on the proprietary microfluidics technology of Xdrop, adding the capability to sort double-emulsion droplets based on the fluorescence of the encapsulated biological material.

Do you want to know more about the Xdrop technology?

Scientific papers

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

Genomics

Generation, quality control, and analysis of the first genomically humanised knock-in mice for the ALS/FTD genes SOD1, TARDBP (TDP-43), and FUS

Anny Devoy, Georgia Price, Francesca De Giorgio, Rosie Bunton-Stasyshyn, David Thompson, Samanta Gasco, Alasdair Allan, Gemma F. Codner, Remya R. Nair, Charlotte Tibbit, Ross McLeod, Zeinab Ali, Judith Noda, Alessandro Marrero-Gagliardi, José M Brito-Armas, Michelle Simon, Edward O’Neill, Jackie Harrison, Gemma Atkins, Silvia Corrochano, Michelle Stewart, Lydia Teboul, Abraham Acevedo-Arozena, Elizabeth M.C Fisher, Thomas J. Cunningham

bioRxiv 2021.07.05.451113; doi: https://doi.org/10.1101/2021.07.05.451113

 

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: https://doi.org/10.1101/2021.07.01.450727

 

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

 

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. Epub 2020 Sep 16. PMID: 32938798.

 

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. Epub 2021 Feb 12. PMID: 33582298.

 

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. Epub 2020 Jun 29. PMID: 32516842; PMCID: PMC7496172.

Cell-based

Long-read whole genome analysis of human single cells

Joanna Hård, Jeff E Mold, Jesper Eisfeldt, Christian Tellgren-Roth, Susana Häggqvist, Ignas Bunikis, Orlando Contreras-Lopez, Chen-Shan Chin, Carl-Johan Rubin, Lars Feuk, Jakob Michaëlsson, Adam Ameur. 2021bioRxiv 2021.04.13.439527; doi: https://doi.org/10.1101/2021.04.13.439527

 

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.

Posters

Poster immune cell potency June 2022

Functional analyses of immune cell potency in droplets

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

phasing

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