Xdrop microfluidics products prepare even small amounts of DNA for highly targeted sequencing.
Xdrop genomics workflows involve encapsulating long DNA fragments in microfluidics droplets and enriching just the target DNA. This allows highly accurate:
Use Xdrop to prepare your DNA for sequencing.
Localizing lentiviral transduction-inserted CAR cassettes in T cells using Xdrop®.
Starting from just 10 ng of DNA, Xdrop reveals gene cassettes inserted using lentivirus and other transduction systems.
Here, Xdrop reveals 1,000 unique insertion sites of the CAR cassette inserted all over the genome.
Verifying CRISPR editing with Xdrop® enables the detection of unintended off-target rearrangements.
Figure: Depth of coverage of Illumina (blue) and Oxford Nanopore (green) sequencing data (sample ε2/ε2). The main graph focuses on the 100 kb surrounding the detection sequence designed to capture the APOE gene region. The inset zooms in on the central 10 kb surrounding the detection sequence.
Detecting HPV18 integration sites in the human genome using Xdrop®.
Targeted DNA enrichment is often necessary to sequence viral integration sites within complex DNA regions. However, available enrichment methods often fail with high- complexity, unknown, or rearranged regions.
Resolving repetitive and GC-rich regions with Xdrop®: Indirect Sequence Capture on Epstein Barr Virus (EBV).
EBV has been associated with several cancers as well as a wide range of other serious diseases. However, the genomic characteristics of the EBV are relatively poorly understood. Here, we use Xdrop for enriching a repetitive and GC-rich region of the EBV from a complex sample. We resolve the sequence of a previously unknown genomic region demonstrating that Xdrop enables the study of complex genomic regions.
Analysis of transgene insertion sites and patterns remains challenging and laborious using current technologies.
Here, with a single primer set and low amount of input DNA, we identify the insertion sites and characterize the surrounding genomic landscapes of a transgene.
The Xdrop Sort workflow combined with long-read sequencing simplifies the identification of both insertion sites and patterns.
Revealing the structure of a biosynthetic gene cluster in a barley variety using Xdrop® and nanopore sequencing.
Xdrop enriches specific genomic regions inplant varieties, enabling in-depth sequence elucidation.
Here, Xdrop is used in aworkflow to reveal the structure of a biosynthetic gene cluster in a barley variety with no reference genome.
Closing gaps in the sequence of a biosynthetic gene cluster in a tomato variety using Xdrop®.
Whole genome sequencing is not the ideal method to close gaps in gene cluster sequences.
Xdrop supports targeted and efficient gap closing.
Here, Xdrop is used to close gaps in the structure of a biosynthetic gene cluster in a tomato variety with excellent coverage and accuracy.
Click on a headline to open up more about posters.
Supporting engineered cell therapy: targeted and accurate assessments of gene editing outcomes with Xdrop® and long-read sequencing
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
Click on a headline to open up more info about scientific papers.
2024
Pushing the limits of single molecule transcript sequencing to uncover the largest disease-associated transcript isoforms in the humanneural retinal
Merel Stemerdink, Tabea Riepe, Nick Zomer, et al.
DOI: 10.1101/2024.09.10.612265. This article is a preprint and has not been certified by peer review.
Single cell long read whole genome sequencing reveals somatic transposon activity in human brain
Michal B Izydorczyk, Ester Kalef-Ezra, Dominic W Horner, et al.
medRxiv 2024.11.11.24317113; doi: https://doi.org/10.1101/2024.11.11.24317113 This article is a preprint and has not been certified by peer review.
Taf1 knockout is lethal in embryonic male mice and heterozygous females show weight and movement disorders
Elisa M. Crombie, Andrea J. Korecki, Karen Cleverley, et al.
Dis Model Mech (2024), dmm.050741. DOI: 10.1242/dmm.050741
T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix Xdrop® enrichment technology
Zarka, K. A., Jagd, L. M. & Douches, D. S.
Front Plant Sci 15, (2024); DOI: 10.3389/fpls.2024.1330429
2023
Droplet-based whole genome amplification: a novel approach for sequencing minute amounts of Mycobacterium tuberculosis DNA
Anzaan Dippenaar, Nabila Ismail, Tim H Heupink et al.
November 2023, PREPRINT available at Research Square; DOI: 10.21203/rs.3.rs-3655355
Long-read whole genome analysis of human single cells
Hård, J., Mold, J.E., Eisfeldt, J. et al.
Nat Commun 14, 5164 (2023). DOI: 10.1038/s41467-023-40898-3
A cis-regulatory point mutation at a R2R3-Myb transcription factor contributes to speciation by reinforcement in Phlox drummondii
Austin G. Garner, Andrew Cameron, Andrea E. Berardi, Robin Hopkins
bioRxiv 2023.04.19.537550; DOI: 10.1101/2023.04.19.537550
A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors.
Tomaž Š, Petek M, Lukan T, Pogačar K, Stare K, Teixeira PE, Jacobson DA, Zrimec J, Bajc G, Butala M, Pompe Novak M, Dudley Q, Patron N, Taler-Verčič A, Usenik A, Turk D, Prat S, Coll A, Gruden K.
Plant Physiol. 2023 Mar 17;191(3):1934-1952. DOI: 10.1093/plphys/kiac579
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: 10.21203/rs.3.rs-2179710/v1
2022
CRISPR-Powered Microfluidics in Diagnostics: A Review of Main Applications
Azimzadeh, Mostafa, Marziyeh Mousazadeh, Atieh Jahangiri-Manesh, Pouria Khashayar, and Patricia Khashayar.
Chemosensors. 2022; 10(1):3. DOI: 10.3390/chemosensors10010003
Unraveling Structural Rearrangements of the CFH Gene Cluster in Atypical Hemolytic Uremic Syndrome Patients Using Molecular Combing and Long-Fragment Targeted Sequencing.
Tschernoster N, Erger F, Walsh PR, McNicholas B, Fistrek M, Habbig S, Schumacher AL, Folz-Donahue K, Kukat C, Toliat MR, Becker C, Thiele H, Kavanagh D, Nürnberg P, Beck BB, Altmüller J.
J Mol Diagn. 2022 Jun;24(6):619-631. DOI: 10.1016/j.jmoldx.2022.02.006
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). 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; 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: 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.
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
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.
Transform discovery workflows. Effortlessly encapsulate single-cell libraries, enhancing the speed of your screening campaigns.
Elevate cell line development workflow. Encapsulate and screen single mammalian cells for enhanced antibody production.
Explore immune cell function in single-cell format assays, including cytokine, granzyme B, and cell killing assays.
