A5031365508- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Cancer Genomics and Diagnostics
- Extracellular vesicles in disease
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Environmental DNA in Biodiversity Studies
- Genetics and Neurodevelopmental Disorders
- RNA modifications and cancer
- Biochemical Analysis and Sensing Techniques
- Chromosomal and Genetic Variations
- Pluripotent Stem Cells Research
- Hearing, Cochlea, Tinnitus, Genetics
- Advanced biosensing and bioanalysis techniques
- Genomics and Chromatin Dynamics
- Plant and Fungal Interactions Research
- Context-Aware Activity Recognition Systems
- DNA Repair Mechanisms
- Hematopoietic Stem Cell Transplantation
- Gut microbiota and health
- Genetics, Aging, and Longevity in Model Organisms
Ludwig-Maximilians-Universität München
2015-2025
Genomics (United Kingdom)
2019-2025
Karolinska Institutet
2019-2022
LMU Klinikum
2019
Max Planck Institute for Biology of Ageing
2019
Max Planck Society
2014
Max Planck Institute for Evolutionary Anthropology
2014
Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification the cDNA. The high throughput is made possible by early introduction sample-specific bar codes (BCs), and bias alleviated unique molecular identifiers (UMIs). Thus, ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according both BC UMI.
The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a large variety experimental and computational pipelines for which best practices have not yet been established. Here, we use simulations based on five scRNA-seq library protocols in combination with nine realistic differential expression (DE) setups to systematically evaluate three mapping, four imputation, seven normalisation testing approaches resulting ~3000 pipelines, allowing us also assess...
Abstract Currently, quantitative RNA-seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and this affects precision accuracy quantification. To assess the effects amplification, reads originated from same molecule (PCR-duplicates) need be identified. Computationally, read duplicates defined by their mapping position, which does not distinguish PCR- natural hence treat...
Abstract Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility, cost-efficiency can advance many research questions. Among the flexible plate-based methods, single-cell barcoding (SCRB-seq) is highly sensitive efficient. Here, we systematically evaluate experimental conditions of this protocol find that adding polyethylene glycol considerably increases...
Power analysis is essential to optimize the design of RNA-seq experiments and assess compare power detect differentially expressed genes in data. PowsimR a flexible tool simulate evaluate differential expression from bulk especially single-cell data making it suitable for priori posterior analyses.The R package associated tutorial are freely available at https://github.com/bvieth/powsimR.vieth@bio.lmu.de or hellmann@bio.lmu.de.Supplementary Bioinformatics online.
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard method, but is fourfold more cost-efficient due almost 50-fold cheaper costs. also direct isolation step, intronic reads are derived from RNA, compare cost-efficiencies of available protocols. conclude prime-seq currently one the best options set up protocol...
In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage cell-free ambient RNA or swapping events.
Induced pluripotent stem cells (iPSCs) are regarded as a central tool to understand human biology in health and disease.Similarly, iPSCs from non-human primates should be evolution, particular for assessing the conservation of regulatory networks iPSC models.Here, we have generated human, gorilla, bonobo cynomolgus monkey assess their usefulness such framework.We show that these well comparable differentiation potential generally similar rhesus embryonic (ESCs).RNA sequencing reveals...
Here, we show that the Wnt5a-haploinsufficient niche regenerates dysfunctional HSCs, which do not successfully engraft in secondary recipients. RNA sequencing of regenerated donor Lin− SCA-1+ KIT+ (LSK) cells shows dysregulated expression ZEB1-associated genes involved small GTPase-dependent actin polymerization pathway. Misexpression DOCK2, WAVE2, and activation CDC42 results apolar F-actin localization, leading to defects adhesion, migration homing HSCs a microenvironment. Moreover, these...
Abstract Background Single-cell RNA sequencing (scRNA-seq) offers exciting possibilities to address biological and medical questions, but a systematic comparison of recently developed protocols is still lacking. Results We generated data from 447 mouse embryonic stem cells using Drop-seq, SCRB-seq, Smart-seq (on Fluidigm C1) Smart-seq2 analyzed existing 35 prepared with CEL-seq. find that the most sensitive method as it detects genes per cell across cells. However, shows more amplification...
Abstract The integration of multimodal single-cell data enables comprehensive organ reference atlases, yet its impact remains largely unexplored, particularly in complex tissues. We generated a benchmarking dataset for the renal cortex by integrating 3’ and 5’ scRNA-seq with joint snRNA-seq snATAC-seq, profiling 119,744 high-quality nuclei/cells from 19 donors. To align cell identities enable consistent comparisons, we developed interpretable machine learning tool scOMM (single-cell Omics...
The identification of cell types remains a major challenge. Even after decade single-cell RNA sequencing (scRNA-seq), reasonable type annotations almost always include manual non-automated steps. orthologous across species complicates matters even more, but at the same time strengthens confidence in assignment. Here, we generate and analyze dataset consisting embryoid bodies (EBs) derived from induced pluripotent stem cells (iPSCs) four primate species: humans, orangutans, cynomolgus, rhesus...
The identification of cell types remains a major challenge. Even after decade single-cell RNA sequencing (scRNA-seq), reasonable type annotations almost always include manual non-automated steps. orthologous across species complicates matters even more, but at the same time strengthens confidence in assignment. Here, we generate and analyze dataset consisting embryoid bodies (EBs) derived from induced pluripotent stem cells (iPSCs) four primate species: humans, orangutans, cynomolgus, rhesus...
Genetic disruptions of the forkhead box transcription factor FOXP2 in humans cause an autosomal-dominant speech and language disorder. While expression pattern are highly conserved, its role specific brain areas for mammalian social behaviors remains largely unknown. Here we studied mice carrying a homozygous cortical Foxp2 deletion. The postnatal development gross morphological architecture mutant was indistinguishable from wildtype (WT) littermates. Unbiased behavioral profiling adult...
Pleiotropy, measured as expression breadth across tissues, is one of the best predictors for protein sequence and conservation. In this study, we investigated its effect on evolution cis -regulatory elements (CREs). To end, carefully reanalyzed Epigenomics Roadmap data nine fetal assigning a measure pleiotropic degree to nearly half million CREs. assess functional conservation CREs, generated ATAC-seq RNA-seq from humans macaques. We found that more CREs exhibit greater in accessibility,...
Abstract Single cell RNA-seq (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification the cDNA. The high throughput is made possible by early introduction sample-specific barcodes (BCs) and bias alleviated unique molecular identifiers (UMIs). Thus ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according both BC UMI. zUMIs such a pipeline, it can handle known random BCs also collapses UMIs, either just Exon mapping Intron...
Brain size and cortical folding have increased decreased recurrently during mammalian evolution. Identifying genetic elements whose sequence or functional properties co-evolve with these traits can provide unique information on evolutionary developmental mechanisms. A good candidate for such a comparative approach is TRNP1 , as it controls proliferation of neural progenitors in mice ferrets. Here, we investigate the contribution both regulatory coding sequences to brain over 30 mammals. We...
ABSTRACT Currently quantitative RNA-Seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and this effects precision accuracy quantification. To assess the amplification, reads originated from same molecule (PCR-duplicates) need be identified. Computationally, read duplicates defined via their mapping position, which does not distinguish PCR- natural hence treat...
Abstract Power analysis is essential to optimize the design of RNA-seq experiments and assess compare power detect differentially expressed genes in data. PowsimR a flexible tool simulate evaluate differential expression from bulk especially single-cell data making it suitable for priori posterior analyses.
Abstract The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a large variety experimental and computational pipelines for which best practices have not been established, yet. Here, we use simulations based on five scRNA-seq library protocols in combination with nine realistic differential expression (DE) setups to systematically evaluate three mapping, four imputation, seven normalisation testing approaches resulting ∼ 3,000 pipelines, allowing us also...
Summary Single-cell RNA sequencing (scRNA-seq) has emerged as the central genome-wide method to characterize cellular identities and processes. While performance of scRNA-seq methods is improving, an optimum in terms sensitivity, cost-efficiency flexibility not yet been reached. Among flexible plate-based “Single-Cell RNA-Barcoding Sequencing” (SCRB-seq) one most sensitive efficient ones. Based on this protocol, we systematically evaluated experimental conditions such reverse transcriptases,...