Discover more about our microfluidics technology and its applications in the Samplix Knowledge Center, which includes webinars, scientific posters, and research papers.
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 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.
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.
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.
Efficiently finding rare active enzyme variants
Quantifying active killer cells with Xdrop
Revealing highly potent secretors of IFN-γ
Single cell assay to quantify IFN-γ and TNF-α secretion
Identifying highly potent TNF-α-secreting T cells from a blood sample
Simplifying transgene insertion analysis with Xdrop® Sort
Verifying CRISPR edits with Xdrop®
Detecting HPV18 integration sites using Xdrop®
Resolving repetitive and GC-rich regions with Xdrop®
Genes vs. pseudogenes
Revealing the structure of a biosynthetic gene cluster
Gap closing in a plant gene cluster
This section includes technical notes describing experiments that establish some of the capabilities of our Xdrop microfluidics system.
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.
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 DE20 and DE50 droplets are compatible with common growth media
Xdrop DE20 and DE50 droplet properties support cell workflows
Improved whole genome amplification with Xdrop
Duplex Xdrop enrichment
Benchmarking 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.
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.
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.
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
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.
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.
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.
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
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.
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."
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."
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.
Talk by ALEX KHITUN, Postdoctoral Researcher at Harvard Medical School
Talk by PETER MOURITZEN, VP Application & Market Development at Samplix
Talk by TOM CUNNINGHAM, Senior Investigator Scientist at MRC Harwell
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
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
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
Click on a headline to open up more info about scientific papers.
2023
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, Jessica Nordlund, Carl-Johan Rubin, Lars Feuk, Jakob Michaëlsson, Adam Ameur
bioRxiv 2021.04.13.439527; doi: https://doi.org/10.1101/2021.04.13.439527
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: https://doi.org/10.21203/rs.3.rs-2179710/v1
2022
Population-wide gene disruption in the murine lung epithelium via AAV-mediated delivery of CRISPR-Cas9 components
Honglin Chen, Steffen Durinck, Hetal Patel, Oded Foreman, Kathryn Mesh, Jeffrey Eastham, Roger Caothien, Robert J Newman, Merone Roose-Girma, Spyros Darmanis, Soren Warming, Annalisa Lattanzi, Yuxin Liang, Benjamin 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 Geng, Lara G Merino, Linda Wedemann, Aniek Martens, Małgorzata Sobota, Yerma P Sanchez, Jonas Nørskov Søndergaard, Robert J White, Claudia Kutter
Genome Res. 2022. 32(10): 1876–1891; doi: 10.1101/gr.276901.122
2021
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, 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: 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
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.
2020
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.
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.
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. 2021
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.
Functional analyses of immune cell potency in droplets
Unbiased Amplification of Single Molecules enables even coverage of chromosomal DNA
Microfluidics based, long fragment, targeted enrichment
Targeted enrichment of long DNA-molecules by droplet sorting for phasing mutation in TP53
