Christoph Muus

Single cell profiling of human airway identifies tuft-ionocyte progenitor cells displaying cytokine-dependent differentiation bias in vitro

Viral S. Shah, Avinash Waghray, Brian Lin, Atharva Bhagwat et autres

Human airways contain specialized rare epithelial cells including CFTR-rich ionocytes that regulate airway surface physiology and chemosensory tuft cells that produce asthma-associated inflammatory mediators. Here, using a lung cell atlas of 311,748 single cell RNA-Seq profiles, we identify 687 ionocytes (0.45%). In …

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A deep lung cell atlas reveals cytokine-mediated lineage switching of a rare cell progenitor of the human airway epithelium

Avinash Waghray, Isha Monga, Brian Lin, Viral S. Shah et autres

Abstract The human airway contains specialized rare epithelial cells whose roles in respiratory disease are not well understood. Ionocytes express the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), while chemosensory tuft cells express asthma-associated alarmins. However, surprisingly, exceedingly few mature tuft cells have …

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Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

Caleb A. Lareau, Leif S. Ludwig, Christoph Muus, Satyen Harish Gohil et autres

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Systematic benchmarking of single-cell ATAC-sequencing protocols

Florian V. De Rop, Gert J. Hulselmans, Christopher Flerin, Paula Soler-Vila et autres

Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight …

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Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells

Caleb A. Lareau, Sonia M. Dubois, Frank A. Buquicchio, Yu-Hsin Hsieh et autres

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Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics

David B. Morse, Aleksandra M. Michalowski, Michele Ceribelli, Joachim De Jonghe et autres

Single-cell RNA sequencing (scRNA-seq) is a powerful technique for describing cell states. Identifying the spatial arrangement of these states in tissues remains challenging, with the existing methods requiring niche methodologies and expertise. Here, we describe segmentation by exogenous perfusion (SEEP), a rapid …

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Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

Caleb A. Lareau, Vincent Liu, Christoph Muus, Samantha D. Praktiknjo et autres

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Single-cell multi-omics reveals dynamics of purifying selection of pathogenic mitochondrial DNA across human immune cells

Caleb A. Lareau, Sonia M. Dubois, Frank A. Buquicchio, Yu-Hsin Hsieh et autres

Abstract Cells experience intrinsic and extrinsic pressures that affect their proclivity to expand and persist in vivo . In congenital disorders caused by loss-of-function mutations in mitochondrial DNA (mtDNA), metabolic vulnerabilities may result in cell-type specific phenotypes and depletion of pathogenic alleles, …

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Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1

Leif S. Ludwig, Caleb A. Lareau, Erik L. Bao, Nan Liu et autres

Master regulators, such as the hematopoietic transcription factor (TF) GATA1, play an essential role in orchestrating lineage commitment and differentiation. However, the precise mechanisms by which such TFs regulate transcription through interactions with specific cis-regulatory elements remain incompletely understood. Here, we describe …

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Processed data supplementary to "Systematic benchmarking of single-cell ATAC sequencing protocols"

Florian V. De Rop, Christopher Flerin, Paula Soler, Albert Rafels et autres

Fragments.tsv.gz for all 15 samples + merged, each for the full sequencing data and library downsampled data (42k reads/cell for each sample). Also contains expression matrices for the multiome (full_10x_Multiome_?_RNA_gex.zip) and 10x scRNA-seq data (10x_scRNA_?_gex.zip).

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Processed data supplementary to "Systematic benchmarking of single-cell ATAC sequencing protocols"

Florian V. De Rop, Christopher Flerin, Paula Soler, Albert Rafels et autres

Fragments.tsv.gz for all 15 samples + merged, each for the full sequencing data and library downsampled data (42k reads/cell for each sample). Also contains expression matrices for the multiome (full_10x_Multiome_?_RNA_gex.zip) and 10x scRNA-seq data (10x_scRNA_?_gex.zip).

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Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

Ronan Chaligné, Federico Gaiti, Dana Silverbush, Joshua S. Schiffman et autres

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