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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...
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Article
Open AccessAn automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Sequencing the nucleic acid content of individual cells or specific biological samples is becoming increasingly common. This drives the need for robust, scalable and automated library preparation protocols. Fu...
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Open AccessCorrection: Corrigendum: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Scientific Reports 6: Article number: 37137; published online: 16 November 2016; updated: 13 March 2017 This Article contains errors in Figure 6c. The Pearson correlation values for the automated and manually ...
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Spatially resolved transcriptome profiling in model plant species
Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profile...
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Article
Open AccessSpatial detection of fetal marker genes expressed at low level in adult human heart tissue
Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate ...
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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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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
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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Open AccessExploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Lately it has become possible to analyze transcriptomic profiles in tissue sections with retained cellular context. We aimed to explore synovial biopsies from rheumatoid arthritis (RA) and spondyloarthritis (S...
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Article
Open AccessIdentification and transfer of spatial transcriptomics signatures for cancer diagnosis
Distinguishing ductal carcinoma in situ (DCIS) from invasive ductal carcinoma (IDC) regions in clinical biopsies constitutes a diagnostic challenge. Spatial transcriptomics (ST) is an in situ capturing method,...
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Open AccessThree-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium
The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area. Rheumatoid ar...
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Open AccessIntegrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis
B cells play a significant role in established Rheumatoid Arthritis (RA). However, it is unclear to what extent differentiated B cells are present in joint tissue already at the onset of disease. Here, we stud...
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Open AccessAn integrated single cell and spatial transcriptomic map of human white adipose tissue
To date, single-cell studies of human white adipose tissue (WAT) have been based on small cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a comprehensive meta-analysis of publi...
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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 AccessMap** spatially resolved transcriptomes in human and mouse pulmonary fibrosis
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathog...
