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Article
Open AccessTools for microbial single-cell genomics for obtaining uncultured microbial genomes
The advent of next-generation sequencing technologies has facilitated the acquisition of large amounts of DNA sequence data at a relatively low cost, leading to numerous breakthroughs in decoding microbial gen...
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Article
Open AccessTargeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral
Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of En...
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Article
Open AccessReproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis
Spatial transcriptome analysis of formalin-fixed paraffin-embedded (FFPE) tissues using RNA-sequencing (RNA-seq) provides interactive information on morphology and gene expression, which is useful for clinical...
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Article
Open AccessStrain-level profiling of viable microbial community by selective single-cell genome sequencing
Culture-independent analysis with high-throughput sequencing has been widely used to characterize bacterial communities. However, signals derived from non-viable bacteria and non-cell DNA may inhibit its chara...
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Article
Open AccessRecovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics
Obtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite improvements in ...
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Open AccessEvaluation of the effects of cell-dispensing using an inkjet-based bioprinter on cell integrity by RNA-seq analysis
Bioprinting technology is expected to be applied in the fields of regenerative medicine and drug discovery. There are several types of bioprinters, especially inkjet-based bioprinter, which can be used not onl...
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Open AccessEffective microtissue RNA extraction coupled with Smart-seq2 for reproducible and robust spatial transcriptome analysis
Spatial transcriptomics is useful for understanding the molecular organization of a tissue and providing insights into cellular function in a morphological context. In order to obtain reproducible results in s...
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Article
Open AccessTime-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast
How quiescent cells break dormancy is a key issue in eukaryotic cells including cancer. Fungal spores, for example, remain quiescent for long periods until nourished, although the mechanisms by which dormancy ...
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Open AccessSingle-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota
The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabol...
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Article
Open AccessHigh-throughput identification of peptide agonists against GPCRs by co-culture of mammalian reporter cells and peptide-secreting yeast cells using droplet microfluidics
Since G-protein coupled receptors (GPCRs) are linked to various diseases, screening of functional ligands against GPCRs is vital for drug discovery. In the present study, we developed a high-throughput functio...
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Article
Open AccessCorrection to: A CCR5+ memory subset within HIV-1-infected primary resting CD4+ T cells is permissive for replication-competent, latently infected viruses in vitro
After publication of the original article [1], the authors became aware of a miscalculation in the original Fig. 2d.
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Open AccessA CCR5+ memory subset within HIV-1-infected primary resting CD4+ T cells is permissive for replication-competent, latently infected viruses in vitro
Resting CD4+ T cells are major reservoirs of latent HIV-1 infection, and may be formed during the early phase of the infection. Although CCR5-tropic (R5) HIV-1 is highly transmissible during the early phase, newl...
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Open AccessCombinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
Single-cell RNA-seq is a powerful tool for revealing heterogeneity in cancer cells. However, each of the current single-cell RNA-seq platforms has inherent advantages and disadvantages. Here, we show that comb...
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Open AccessObtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes
Single-cell genomics is a straightforward approach to obtain genomes from uncultured microbes. However, sequence reads from a single-cell amplified genome (SAG) contain significant bias and chimeric sequences....
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Open AccessMassively parallel whole genome amplification for single-cell sequencing using droplet microfluidics
Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequenci...
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Article
Open AccessSite-specific gene expression analysis using an automated tissue micro-dissection punching system
Site-specific gene expression analyses are important for understanding tissue functions. Despite rapid developments in DNA-related technologies, the site-specific analysis of whole genome expression for a tiss...
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Article
Efficient DNA release from PAMAM dendrimer-modified superparamagnetic nanoparticles for DNA recovery
DNA recovery using solid-phase extraction is a fundamental technique in molecular biology and biotechnology. Our research group developed a novel DNA recovery method using amine-modified magnetic nanoparticles...
