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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...
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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 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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Article
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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Article
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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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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Article
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 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
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
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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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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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...
