Discover more about our microfluidics technology and its applications in the Samplix Knowledge Center, which includes webinars, scientific posters, and research papers.
This page shows examples and application notes to demonstrate some of the capabilities of the Samplix Xdrop.
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.
Verifying CRISPR edits with Xdrop®
Finding transgene insertion sites
Virus Integration Detection
Genes vs. pseudogenes
Revealing the structure of a biosynthetic gene cluster
Gap closing in a plant gene cluster
At ESHG 2022 in Vienna, Samplix hosted a special event where three experts talked on a 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
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?
Click on a headline to open up more info about scientific papers.
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.
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.
Microfluidics based, long fragment, targeted enrichment
Targeted enrichment of Long DNA-molecules by droplet sorting for phasing mutation in TP53
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