小柯机器人

美国俄勒冈州健康与科学大学Andrew C. Adey课题组开发出高内涵单细胞组合索引技术。这一研究成果于2021年7月5日在线发表在国际学术期刊《自然—生物技术》上。

据研究人员介绍，单细胞组合索引（sci）与基于转座酶的文库构建增加了单细胞基因组学检测的通量，但在每个细胞的可用读数方面仅能够较少获取。

研究人员开发了对称链sci（‘s3’），这是一种基于尿嘧啶的接头切换方法，可提高源DNA在标记后转化为可行的测序文库片段的速度。研究人员将此化学应用于人类皮层和小鼠全脑组织中的染色质可及性分析（s3-assay for transposase-accessible chromatin, s3-ATAC），与其他可用的方法相比，每个细胞的可用读数提高了6到13倍。与sci-DNA测序和sci-HiC相比，将s3应用于单细胞全基因组测序（s3-WGS）和全基因组加染色质构象（s3-GCC）分别使每个细胞的可用读数提高了148倍和14.8倍。

结果表明s3-WGS和s3-GCC能够解析患者来源胰腺癌细胞系中的亚克隆基因组改变。研究人员预计s3平台将与其他基于转座酶的技术兼容，包括sci-MET或CUT&Tag。

附：英文原文

Title: High-content single-cell combinatorial indexing

Author: Ryan M. Mulqueen, Dmitry Pokholok, Brendan L. OConnell, Casey A. Thornton, Fan Zhang, Brian J. ORoak, Jason Link, Galip Grkan Yardmc, Rosalie C. Sears, Frank J. Steemers, Andrew C. Adey

Issue&Volume: 2021-07-05

Abstract: Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but produces sparse coverage in terms of usable reads per cell. We develop symmetrical strand sci (‘s3’), a uracil-based adapter switching approach that improves the rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-assay for transposase-accessible chromatin, s3-ATAC) in human cortical and mouse whole-brain tissues, with mouse datasets demonstrating a six- to 13-fold improvement in usable reads per cell compared with other available methods. Application of s3 to single-cell whole-genome sequencing (s3-WGS) and to whole-genome plus chromatin conformation (s3-GCC) yields 148- and 14.8-fold improvements, respectively, in usable reads per cell compared with sci-DNA-sequencing and sci-HiC. We show that s3-WGS and s3-GCC resolve subclonal genomic alterations in patient-derived pancreatic cancer cell lines. We expect that the s3 platform will be compatible with other transposase-based techniques, including sci-MET or CUT&Tag.

DOI: 10.1038/s41587-021-00962-z

Source: https://www.nature.com/articles/s41587-021-00962-z

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex