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1.
Bioinformatics ; 36(12): 3905-3906, 2020 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-32330223

RESUMO

SUMMARY: Bulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and allele-specific fashion. Single-cell gene expression assays have the potential to further resolve these expression patterns, but currently available methods do not perform allele-specific quantification at the molecule level. Here, we present scHLAcount, a post-processing workflow for single-cell RNA-seq data that computes allele-specific molecule counts of the HLA genes based on a personalized reference constructed from the sample's HLA genotypes. AVAILABILITY AND IMPLEMENTATION: scHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Análise de Célula Única , Software , Alelos , Expressão Gênica , Humanos , Análise de Sequência de RNA , Fluxo de Trabalho
2.
Proc Natl Acad Sci U S A ; 105(4): 1176-81, 2008 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-18216253

RESUMO

Optical nanostructures have enabled the creation of subdiffraction detection volumes for single-molecule fluorescence microscopy. Their applicability is extended by the ability to place molecules in the confined observation volume without interfering with their biological function. Here, we demonstrate that processive DNA synthesis thousands of bases in length was carried out by individual DNA polymerase molecules immobilized in the observation volumes of zero-mode waveguides (ZMWs) in high-density arrays. Selective immobilization of polymerase to the fused silica floor of the ZMW was achieved by passivation of the metal cladding surface using polyphosphonate chemistry, producing enzyme density contrasts of glass over aluminum in excess of 400:1. Yields of single-molecule occupancies of approximately 30% were obtained for a range of ZMW diameters (70-100 nm). Results presented here support the application of immobilized single DNA polymerases in ZMW arrays for long-read-length DNA sequencing.


Assuntos
Alumínio , RNA Polimerases Dirigidas por DNA/química , Enzimas Imobilizadas/química , Nanoestruturas/química , Óptica e Fotônica , Análise Serial de Proteínas/instrumentação , Análise Serial de Proteínas/métodos , DNA Circular/química , RNA Polimerases Dirigidas por DNA/isolamento & purificação , Vidro , Microscopia de Fluorescência/instrumentação , Microscopia de Fluorescência/métodos , Organofosfonatos/química , Polivinil/química , Propriedades de Superfície , Moldes Genéticos
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