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:
Efficiently screening for rare, active enzyme variants

Library sizes of >1012 enzyme variants can be generated during enzyme engineering. However, conventional microtiter plate- or agar plate-based screening systems only allow a few thousand variants to be screened, leaving most of the generated variants unexplored.

Samplix has developed a workflow using Xdrop and the Xdrop DE20 Cartridge to encapsulate living bacterial cells producing an enzyme library with rare active variants in DE20 droplets.

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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Efficiently finding rare active enzyme variants

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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 that secrete IFN-γ, TNF-α, or both in a single-cell 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

Technical notes

This section includes technical notes describing experiments that establish some of the capabilities of our Xdrop microfluidics system.

Featured technical note for functional analysis of cells:
DE20 and DE50 droplets are compatible with common growth media

Here, we report on the compatibility of Xdrop double-emulsion droplets (DE20 and DE50 droplets) with various media for growing bacteria,fungi, or mammalian cells as well as some solutions commonly used in cell biology.

The high success rate for droplet generation demonstrates that the Xdrop double-emulsion droplet system has the potential to encapsulate living bacterial, yeast or mammalian cells with a wide variety of growth media. 

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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Xdrop DE20 and DE50 droplets are compatible with common growth media

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Xdrop DE20 and DE50 droplet properties support cell workflows

Samplix Xdrop TechNote Improved WGA Jan 2022

Improved whole genome amplification with Xdrop

BRCA2 Milestones Tech note V1.0

Duplex Xdrop enrichment

2007 Samplix technote benchmarking v1.0

Benchmarking Xdrop

Webinars

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

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

Scientific papers

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

Genomics

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. 27: 431–449; doi: 10.1016/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; doi: 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, 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

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: 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