ddSEQ™ Single-Cell Isolator from Bio-Rad

Product Specs
ItemddSEQ™ Single-Cell Isolator
CompanyBio-Rad
Price Get Pricing
Catalog Number12004336
TypeSingle-Cell Isolator
ThroughputProcess hundreds to tens of thousands of cells per day
Data AnalysisSecondary analysis processed by Bio-Rad’s Omnition Analysis software

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Bio-Rad

Bio-Rad Laboratories, Inc. Life Science Research Group 2000 Alfred Nobel Drive

Hercules, California 94547

United States

Phone: 800-424 6723
800-879 2289

Company Profile

Website: http://discover.bio-rad.com

(1) Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programsJournal of Experimental & Clinical Cancer ResearchFebruary 11, 2026Takaaki Furukawa, Kohei Kumegawa, Kenichi Miyata, Manabu Takamatsu, Asumi Iesato, Sumito Saeki, Liying Yang, Chikako Shibata, Tomoko Takahara, Kaoru Masuda, et al.detailed methods are provided below. Single-cell ATAC sequencing scATAC-seq was conducted using the ddSEQ Single-Cell Isolator (Bio-Rad), and data were analyzed using ArchR (v1.0.2) in accordance with a previous study [15]. Quality

(2) Characterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancerGenome MedicineNovember 27, 2025Chisa Hori, Kohei Kumegawa, Sumito Saeki, Yoko Takahashi, Liying Yang, Tomoyoshi Nakadai, Kazutaka Otsuji, Chikako Takahata, Yukinori Ozaki, Natsue Uehiro, et al.indexed-Tn5, the library was prepared using the SureCell ATAC-Seq Library Prep Kit (Bio-Rad) and a ddSEQ Single-Cell Isolator system (Bio-Rad). Q5 HiFi DNA Polymerase and USER II Enzyme (both from NEB) were used for a subset of

(3) Single-cell transcriptomics reveals biomarker heterogeneity linked to CDK4/6 Inhibitor resistance in breast cancer cell linesnpj Breast CancerJuly 31, 2025Ilenia Migliaccio, Martina Bonechi, Dario Romagnoli, Giulia Boccalini, Francesca Galardi, Cristina Guarducci, Agostina Nardone, Rachel Schiff, Laura Biganzoli, Luca Malorni, et al.were prepared and loaded into the ddSEQ cartridges to generate the single cell droplets by Bio-Rad ddSEQ single cell isolator, which allows the isolation and barcoding of about 300 cells per well43. For each cell line, at least

(4) Dissecting FAP+ Cell Diversity in Pancreatic Cancer Uncovers an Interferon-Response Subtype of Cancer-Associated Fibroblasts with Tumor-Restraining PropertiesCancer researchJuly 2, 2025Cumming J, Maneshi P, Dongre M, Alsaed T, Dehghan-Nayeri MJ, Ling A, Pietras K, Patthey C, Öhlund D.Library Prep Kit (6-cartridge kit; Illumina Bio-Rad SureCell, 20014280). Single-cells were captured using the ddSeq Single-Cell Isolator (Bio-Rad). Following single-cell capture, libraries were generated according to the manufacturer’s instructions

(5) Single-Cell RNA Sequencing Analysis Reveals Exercise-Induced Transcriptional Dynamics in Half-Marathon RunnersScand J Med Sci SportsJanuary 16, 2025Laura Veschetti, Cristina Patuzzo, Mirko Treccani, Lucas Moron Dalla Tor, Michela Deiana, Samuele Cheri, Francesca Griggio, Giuseppe Lippi, Federico Schena, Daniele De Santis, et al.Library Preparation and Sequencing RNA‐Seq libraries from single PBMCs were prepared using Bio‐Rad ddSEQ Single‐Cell Isolator and reagents provided in the Illumina Bio‐Rad SureCell WTA 3' Library Prep Kit. Briefly, single PBMCs

(6) Modulation of Neuronal Excitability and Plasticity by BHLHE41 Conveys Lithium Non-ResponsivenessbioRxivJuly 30, 2024Marius Stephan, Sergi Papiol, Mingyue Zhang, Jie Song, Samuel M. Frommeyer, Helen Haupt, Niels Jensen, Nirmal Kannaiyan, Rajinder Gupta, Philipp Schuler, et al.Preparation Single-cell libraries were prepared according to manufacturer protocols (Illumina) and isolated using a ddSEQ Single-Cell Isolator (Bio-Rad) or the chromium controller (10x Genomics). Libraries were prepared following the manufacturer’s

(7) Systematic benchmarking of single-cell ATAC-sequencing protocolsNature BiotechnologyJune 1, 2024Florian V. De Rop, Gert Hulselmans, Chris Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo González-Blas, Domenica Marchese, Ginevra Caratù, Suresh Poovathingal, et al.were kept on ice before encapsulation. Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). For samples ddS H1, ddS H2, ddS U1 and ddS U2, 5,000 nuclei were loaded with the goal of

(8) Cell of origin epigenetic priming determines susceptibility to Tet2 mutationNature CommunicationsMay 21, 2024Giulia Schiroli, Vinay Kartha, Fabiana M. Duarte, Trine A. Kristiansen, Christina Mayerhofer, Rojesh Shrestha, Andrew Earl, Yan Hu, Tristan Tay, Catherine Rhee, et al.kept on ice prior to encapsulation. Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit

(9) The single-cell chromatin landscape in gonadal cell lineage specificationBMC GenomicsMay 13, 2024Hoi Ching Suen, Fanghong Ou, Kai-kei Miu, Zhangting Wang, Wai-yee Chan, Jinyue Liaoencapsulation. scATAC-seq library preparation and sequencing Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17,004,620,

(10) Mapping Cell Atlases at the Single‐Cell LevelAdvanced ScienceFebruary 1, 2024Fang Ye, Jingjing Wang, Jiaqi Li, Yuqing Mei, Guoji Guocells. Other commercialized microfluidic droplet platforms such as WaferGen ICELL8[ 14 ] and Bio‐Rad ddSEQ Single‐Cell Isolator[ 15 ] have limitations in throughput, which limits their application in cell atlas construction. Microwell‐based

(11) The single-cell chromatin accessibility landscape in mouse perinatal testis developmenteLifeApril 25, 2023Suen HC, Rao S, Luk ACS, Zhang R, Yang L, Qi H, So HC, Hobbs RM, Lee TL, Liao J.ice before encapsulation. Library preparation and sequencing Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620,

(12) Cellular senescence in malignant cells promotes tumor progression in mouse and patient GlioblastomaNature CommunicationsJanuary 27, 2023Rana Salam, Alexa Saliou, Franck Bielle, Mathilde Bertrand, Christophe Antoniewski, Catherine Carpentier, Agusti Alentorn, Laurent Capelle, Marc Sanson, Emmanuelle Huillard, et al.wells with GFP+ cells or malignant cells and 1 well with GFP− cells or non-malignant cells) on the ddSEQ Single-Cell Isolator (Biorad). A library was generated using SureCell™ Whole Transcriptome Analysis 3′ Library Prep Kit for

(13) scATAC-Seq reveals heterogeneity associated with spermatogonial differentiation in cultured male germline stem cellsScientific ReportsDecember 12, 2022Hoi Ching Suen, Alfred Chun Shui Luk, Jinyue Liaoencapsulation. scATAC-seq library preparation and sequencing Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620,

(14) Recent advances in targeted drug delivery systems for resistant colorectal cancerCancer Cell InternationalDecember 1, 2022Masoumeh Sharifi-Azad, Marziyeh Fathi, William C. Cho, Abolfazl Barzegari, Hamed Dadashi, Mehdi Dadashpour, Rana Jahanban-Esfahlanselection of sequencing platform such as 0X Genomics Chromium, Nadia (Dolomite Bio), Illumina Bio-Rad ddSEQ Single-Cell Isolator, BD Rhapsody Single-Cell Analysis System (BD), ICELL8 Single-cell System (Takara), and Fluidigm C1,

(15) Functional inference of gene regulation using single-cell multi-omicsCell GenomicsSeptember 1, 2022Vinay K. Kartha et al.SureCell ATAC-Seq Library Prep Kit User Guide (17004620, Bio-Rad). Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit

(16) A Detailed Overview About the Single-Cell Analyses of Solid Tumors Focusing on Colorectal CancerPathology and Oncology ResearchJuly 14, 2022William J. Kothalawala, Barbara K. Barták, Zsófia B. Nagy, Sára Zsigrai, Krisztina A. Szigeti, Gábor Valcz, István Takács, Alexandra Kalmár, Béla Molnárbarcoded beads thus enabling parallel sorting of cells and library preparation for NGS. The Bio-Rad ddSEQ Single-Cell Isolator (Bio-Rad Laboratories, Hercules, California, United States) offers a similar technique. Both platforms

(17) Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypesDevelopmentMarch 1, 2022Behzad Yaghmaeian Salmani, Brad Balderson, Susanne Bauer, Helen Ekman, Annika Starkenberg, Thomas Perlmann, Michael Piper, Mikael Bodén, Stefan Thorwere encapsulated into droplets using Bio-Rad ddSEQ Single-Cell Isolator for cell lysis and barcoding (12004336). Subsequently, RNA-seq libraries were generated using SureCell WTA 3′ Library Prep Kit for the ddSEQ

(18) Expression of Lineage Transcription Factors Identifies Differences in Transition States of Induced Human Oligodendrocyte DifferentiationCellsJanuary 11, 2022Raabe FJ, Stephan M, Waldeck JB, Huber V, Demetriou D, Kannaiyan N, Galinski S, Glaser LV, Wehr MC, Ziller MJ, et al.single-cell libraries were prepared with the SureCell WTA 3′ Kit (Illumina, San Diego, CA, USA) on a ddSEQ Single-Cell Isolator (Bio-Rad, Hercules, USA) in accordance with the manufacturer’s protocol. Library quality and yield were

(19) What are the applications of single-cell RNA sequencing in cancer research: a systematic reviewJournal of Experimental & Clinical Cancer ResearchDecember 1, 2021Lvyuan Li et al.single-cell sequencing platforms include the 10X Genomics Chromium, Nadia (Dolomite Bio), Illumina Bio-Rad ddSEQ Single-Cell Isolator, BD Rhapsody Single-Cell Analysis System (BD), ICELL8 Single-cell System (Takara), Fluidigm C1, and

(20) Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapyNature CommunicationsDecember 1, 2021Sara De Biasi et al.mW). Cell sorting was performed with 96-99% purity. Sorted CD3+CD8+ T cells were immediately loaded on ddSEQ single-cell isolator (Bio-Rad Laboratories) to isolate single cells and barcode single cells. sc-RNA-seq libraries were prepared

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