Gain highly targeted insights
from genomics workflows

Xdrop microfluidics products prepare even small amounts
of DNA for highly targeted sequencing.

Use Xdrop for genomics workflows

Xdrop genomics workflows involve encapsulating long DNA fragments in microfluidics droplets and enriching just the target DNA. This allows highly accurate:

  • Validation of gene edits
  • Investigation of unexpected on- and off-target rearrangements
  • Closing gaps in target sequences
  • Resolving tandem repeats
  • Discriminating genes and pseudogenes

Use Xdrop to prepare your DNA for sequencing.

Application notes

CAR insertion sites in engineered genes

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.

Insertion site density

Application notes

Verifying CRISPR edits with Xdrop

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.


Application notes

Detecting viral integrations

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.

Detecting viral integration

Application notes

Resolving repetitive and GC-rich unknown 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.

repetitive gc rich regions

Application note

Simplifying transgene insertion analysis with Xdrop® Sort

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.

Yeast incapsulation

Plant genomics application notes

Revealing a gene cluster structure

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.

Gene cluste

Plant genomics application notes

Gap closing in a plant gene cluster

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.

See the posters
Poster Supporting engineered cell therapy

Supporting engineered cell therapy: targeted and accurate assessments of gene editing outcomes with Xdrop® and long-read sequencing

Poster Unbiased amplification

Unbiased Amplification of Single Molecules enables even coverage of chromosomal DNA

Poster Microfluidics based

Microfluidics based, long fragment, targeted enrichment

Poster with SciLife lab

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

Scientific papers

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

See the papers



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



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/


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


cis-regulatory point mutation at a R2R3-Myb transcription factor contributes to speciation by reinforcement in Phlox drummondii

Austin G. GarnerAndrew CameronAndrea E. BerardiRobin Hopkins


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/ 



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). DOI10.1016/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; DOI10.1101/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; 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.



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.

Discover other applications

Screening box square


Transform discovery workflows. Effortlessly encapsulate single-cell libraries, enhancing the speed of your screening campaigns.

Cell line development box square

Cell line development

Elevate cell line development workflow. Encapsulate and screen single mammalian cells for enhanced antibody production.

Cell therapy box square


Explore immune cell function in single-cell format assays, including cytokine, granzyme B, and cell killing assays.