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10 results for “single cell transcriptome analysis”

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  1. Stratification of enterochromaffin cells by single-cell expression analysis.

    eLife · 2025 · 12

    Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine to mediate disparate physiological responses. However, the molecular and cellular basis for …

    PMID 40184163 DOI ↗

  2. Stratification of enterochromaffin cells by single-cell expression analysis.

    bioRxiv : the preprint server for biology · 2025

    Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine (5-HT) to mediate disparate physiological responses. However, the molecular and cellular basis …

    PMID 37662229 DOI ↗

  3. Bento: a toolkit for subcellular analysis of spatial transcriptomics data.

    Genome biology · 2024 · 25(1): 82

    The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit …

    PMID 38566187 DOI ↗

  4. Antibody-Oligonucleotide Conjugation Using a SPAAC Copper-Free Method Compatible with 10× Genomics' Single-Cell RNA-Seq.

    Methods in molecular biology (Clifton, N.J.) · 2022 · 2463: 67-80

    Recent advances in multimodal approaches toward single-cell analyses present valuable data points that can complement standard flow cytometry data. In particular, the overlay of cell-surface proteome data with gene expression analysis presents a necessary advancement, particularly in the field of …

    PMID 35344168 DOI ↗

  5. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

    Genome biology · 2020 · 21(1): 90

    A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …

    PMID 32252787 DOI ↗

  6. Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.

    Frontiers in molecular neuroscience · 2018 · 11: 261

    The human brain is composed of a complex assembly of about 171 billion heterogeneous cellular units (86 billion neurons and 85 billion non-neuronal glia cells). A comprehensive description of brain cells is necessary to understand the nervous system in health …

    PMID 30147644 DOI ↗

  7. Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.

    Cell metabolism · 2017 · 25(5): 1160-1175.e11

    Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of …

    PMID 28467932 DOI ↗

  8. Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology.

    Molecular psychiatry · 2016 · 21(11): 1573-1588

    Human neural progenitors derived from pluripotent stem cells develop into electrophysiologically active neurons at heterogeneous rates, which can confound disease-relevant discoveries in neurology and psychiatry. By combining patch clamping, morphological and transcriptome analysis on single-human neurons in vitro, we defined …

    PMID 27698428 DOI ↗

  9. Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.

    Genome medicine · 2016 · 8(1): 94

    Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human …

    PMID 27655340 DOI ↗

  10. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

    Nature methods · 2016 · 13(6): 508-14

    As RNA-binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNA molecules, binding site identification by UV crosslinking and immunoprecipitation (CLIP) of ribonucleoprotein complexes is critical to understanding RBP function. However, current CLIP protocols are technically …

    PMID 27018577 DOI ↗

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