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Article
Open AccessHigh clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue
Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly c...
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Article
Open AccessSolid-phase capture and profiling of open chromatin by spatial ATAC
Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chrom...
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Article
Open AccessDRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age
Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their rege...
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Article
Open AccessClonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
The mammalian brain contains many specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Single-cell transcriptomics revealed hundreds of molecularly diverse cell types in the ne...
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Article
Open AccessSpatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell...
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Article
Open AccessPericyte-derived fibrotic scarring is conserved across diverse central nervous system lesions
Fibrotic scar tissue limits central nervous system regeneration in adult mammals. The extent of fibrotic tissue generation and distribution of stromal cells across different lesions in the brain and spinal cor...
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Article
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin
Characterization of the progression of cellular states during human embryogenesis can provide insights into the origin of pediatric diseases. We examined the transcriptional states of neural crest– and mesoder...
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Article
Open AccessThe age of adult pilocytic astrocytoma cells
Adult pilocytic astrocytomas (PAs) have been regarded as indistinguishable from pediatric PAs in terms of genome-wide expression and methylation patterns. It has been unclear whether adult PAs arise early in l...
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Article
Spatially resolved transcriptomics adds a new dimension to genomics
As single-cell omics continue to advance, the field of spatially resolved transcriptomics has emerged with a set of experimental and computational methods to map out the positions of cells and their gene expre...
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Article
Open AccessDistinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
Mature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with diff...
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Chapter
Basic Aspect: Neurorepair After Stroke
This chapter discusses the scientific premise of stem cell-based therapies aimed at repairing damage produced by cerebrovascular insults in the adult human brain. Understanding the principles that govern stem ...
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Article
High-definition spatial transcriptomics for in situ tissue profiling
Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures...
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Article
A fresh look at adult neurogenesis
Improved protocols for the visualization of immature neurons in the human brain provide evidence for generation of neurons in the adult hippocampus and uncover reduced neurogenesis in Alzheimer’s disease.
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Article
Open AccessConbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Accurate variant calling and genoty** represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell ...
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Article
Regenerating the field of cardiovascular cell therapy
The retraction of >30 falsified studies by Anversa et al. has had a disheartening impact on the cardiac cell therapeutics field. The premise of heart muscle regeneration by the transdifferentiation of bone mar...
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Article
Publisher Correction: Dynamics of oligodendrocyte generation in multiple sclerosis
In this Letter, the vertical error bars were missing from Fig. 3b and 3c. This figure has been corrected online.
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Article
Dynamics of oligodendrocyte generation in multiple sclerosis
Oligodendrocytes wrap nerve fibres in the central nervous system with layers of specialized cell membrane to form myelin sheaths1. Myelin is destroyed by the immune system in multiple sclerosis, but myelin is tho...
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Article
Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
Spatial resolution of gene expression enables gene expression events to be pinpointed to a specific location in biological tissue. Spatially resolved gene expression in tissue sections is traditionally analyze...
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Article
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq
Rickard Sandberg and colleagues use allele-sensitive single-cell RNA–seq on primary mouse fibroblasts and human T cells to study clonal and dynamic monoallelic expression patterns. They find that the majority ...
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Article
Open AccessMassive and parallel expression profiling using microarrayed single-cell sequencing
Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost...
