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Methods & Resources

  • High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis
    Open Access
    High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis

    Hiroki Ikeda, Shintaro Miyao, So Nagaoka, Tomoya Takashima, Sze-Ming Law, Takuya Yamamoto, Kazuki Kurimoto

    Hiroki Ikeda ... Kazuki Kurimoto

    Published 18 September 2023

    Quantitative RNA-sequencing method for single cells isolated from alcohol- and formalin-fixed tissue sections discovers new relationships between histology and transcriptome during folliculogenesis.

  • A targeted sequencing extension for transcript genotyping in single-cell transcriptomics
    Open Access
    A targeted sequencing extension for transcript genotyping in single-cell transcriptomics

    Lies Van Horebeek, Margaux David, Nina Dedoncker, Klara Mallants, Baukje Bijnens, An Goris, Bénédicte Dubois

    Lies Van Horebeek ... Bénédicte Dubois

    Published 11 September 2023

    We describe the targeted sequencing extension and provide two proof-of-concept examples of how it can assist with understanding the impact of genetic variants.

  • Refining the genetic risk of breast cancer with rare haplotypes and pattern mining
    Open Access
    Refining the genetic risk of breast cancer with rare haplotypes and pattern mining

    William Letsou, Fan Wang, Wonjong Moon, Cindy Im, Yadav Sapkota, Leslie L Robison, Yutaka Yasui

    William Letsou ... Yutaka Yasui

    Published 4 August 2023

    A closed-pattern mining algorithm helps identify rare, noncontiguous haplotypes underlying breast cancer risk in British women in the UK Biobank.

  • Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope
    Open Access
    Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

    Li-Chun Cheng, Xi Zhang, Sabyasachi Baboo, Julie A Nguyen, Salvador Martinez-Bartolomé, Esther Loose, Jolene Diedrich, John R Yates, Larry Gerace

    Li-Chun Cheng ... Larry Gerace

    Published 11 July 2023

    A cohort of low-abundance transmembrane proteins concentrated at the nuclear envelope has been identified, predicting diverse new functions for this membrane system.

  • Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria
    Open Access
    Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria

    Jun Yong Kim, Ilian Atanassov, Frederik Dethloff, Lara Kroczek, Thomas Langer

    Jun Yong Kim ... Thomas Langer

    Published 15 June 2023

    Time-resolved proteomic analyses of senescent fibroblasts reveal that nearly 40% of the analyzed mitochondrial proteome have changed upon induction of senescence. Our study highlights the rewiring of mitochondrial metabolism as a central feature among all changes in mitochondrial pathways of senescent cells.

  • Estimation of crossbridge-state during cardiomyocyte beating using second harmonic generation
    Open Access
    Estimation of crossbridge-state during cardiomyocyte beating using second harmonic generation

    Hideaki Fujita, Junichi Kaneshiro, Maki Takeda, Kensuke Sasaki, Rikako Yamamoto, Daiki Umetsu, Erina Kuranaga, Shuichiro Higo, Takumi Kondo, Yoshihiro Asano, Yasushi Sakata, Shigeru Miyagawa, Tomonobu M Watanabe

    Hideaki Fujita ... Tomonobu M Watanabe

    Published 26 May 2023

    This article describes a new method to evaluate the actomyosin activity in living cardiomyocytes during beating based on nonlinear scattering microscopy, which will be useful for elucidating cardiomyopathy mechanisms, efficacy of an intervention, and others.

  • BiFCo: visualizing cohesin assembly/disassembly cycle in living cells
    Open Access
    BiFCo: visualizing cohesin assembly/disassembly cycle in living cells

    Emilio González-Martín, Juan Jiménez, Víctor A Tallada

    Emilio González-Martín ... Víctor A Tallada

    Published 9 May 2023

    A novel strategy developed in fission yeast to visualise only-assembled cohesin complex loading/unloading cycles in eukaryotic chromosomes in living cells.

  • Gapless provides combined scaffolding, gap filling, and assembly correction with long reads
    Open Access
    Gapless provides combined scaffolding, gap filling, and assembly correction with long reads

    Stephan Schmeing, Mark D Robinson

    Stephan Schmeing ... Mark D Robinson

    Published 4 May 2023

    gapless is a new tool for combined execution of correction, scaffolding and gap filling using PacBio or Oxford Nanopore reads.

  • Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method
    Open Access
    Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method

    Jianqi Yang, Alison N DeVore, Daniel A Fu, Mackenzie M Spicer, Mengcheng Guo, Samantha G Thompson, Katelin E Ahlers-Dannen, Federica Polato, Andre Nussenzweig, Rory A Fisher

    Jianqi Yang ... Rory A Fisher

    Published 10 April 2023

    A novel, precise, rapid, and generalizable method to determine transgene zygosity in mice by allele-specific restriction enzyme digestion of PCR products from transgenes or homologous endogenous genes.

  • A novel approach to measure complex V ATP hydrolysis in frozen cell lysates and tissue homogenates
    Open Access
    A novel approach to measure complex V ATP hydrolysis in frozen cell lysates and tissue homogenates

    Lucia Fernandez-del-Rio, Cristiane Benincá, Frankie Villalobos, Cynthia Shu, Linsey Stiles, Marc Liesa, Ajit S Divakaruni, Rebeca Acin-Perez, Orian S Shirihai

    Lucia Fernandez-del-Rio ... Orian S Shirihai

    Published 14 March 2023

    This novel method can be used in clinical samples to determine CV function in diseases, with the added benefit of being able to use frozen samples in a high-throughput manner and to explore ATP hydrolysis as a drug target for disease treatment.

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