Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 2 de 2
Filtrar
Más filtros

Banco de datos
Asunto principal
Tipo del documento
País de afiliación
Intervalo de año de publicación
1.
Nat Biotechnol ; 2023 Aug 03.
Artículo en Inglés | MEDLINE | ID: mdl-37537502

RESUMEN

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 scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.

2.
Nat Commun ; 9(1): 994, 2018 03 08.
Artículo en Inglés | MEDLINE | ID: mdl-29520052

RESUMEN

Fundamental research and drug development for personalized medicine necessitates cell cultures from defined genetic backgrounds. However, providing sufficient numbers of authentic cells from individuals poses a challenge. Here, we present a new strategy for rapid cell expansion that overcomes current limitations. Using a small gene library, we expanded primary cells from different tissues, donors, and species. Cell-type-specific regimens that allow the reproducible creation of cell lines were identified. In depth characterization of a series of endothelial and hepatocytic cell lines confirmed phenotypic stability and functionality. Applying this technology enables rapid, efficient, and reliable production of unlimited numbers of personalized cells. As such, these cell systems support mechanistic studies, epidemiological research, and tailored drug development.


Asunto(s)
Transgenes/genética , Animales , Línea Celular , Células Cultivadas , Hepatocitos/citología , Hepatocitos/metabolismo , Humanos , Lentivirus/genética , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Transducción Genética , Transgenes/fisiología
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA