上回书说到,在建库时,单细胞测序通过barcode区分来源不同细胞的RNA序列,但是在同一个细胞中,同一基因可能会产生多次转录,而PCR步骤也会产生重复读取。为了区分reads是来源于生物扩增还是PCR扩增,scRNA-seq采用在PCR扩增前在cDNA序列上引入UMI标记,确定单个cDNA扩增过程中产生的拷贝数。因此scRNA-seq的数据处理有以下几...
Seurat 是一个用于单细胞 RNA 测序 (scRNA-seq) 分析的 R 包。在 Seurat 中,可以使用以下标准来筛选 UMI(Unique Molecular Identifiers): 1. UMI 数量:可以根据 UMI 的数量来筛选细胞。例如,可以过滤掉 UMI 数大于 2500 或小于 200 的细胞。 2. 线粒体基因占比:每个细胞中线粒体基因数目占比超过 5%时,...
Here, we describe the application of UTR-Seq, as a strategy to uncover cis-regulatory signals of RNA stability during early zebrafish embryogenesis. The method combines massively parallel reporter assays (MPRA) with computational regression models. It surveys the effect of tens of thousands of ...
RNA sequencing (RNA-seq) captures the transcriptomic repertoire and quantifies the expression levels of genes. When performed on single cells (scRNA-seq), it is a powerful tool for characterizing cellular heterogeneity and understanding complex biological proces...
Single-cell RNA-Seq (scRNA-Seq) profiles gene expression of individual cells. Recent scRNA-Seq datasets have incorporated unique molecular identifiers (UMIs). Using negative controls, we show UMI counts follow multinomial sampling with no zero inflation. Current normalization procedures such as log of...
Hi. Thanks for creating this tool. I'm trying to do an analysis from a pre-print on some scRNA-seq data and I think UMI Tools might be appropriate. Here is the paper: http://biorxiv.org/content/early/2017/02/02/104844 Basically, there is...
UMI-tools作为一款专为处理带有UMI标签的RNA-seq数据设计的工具,凭借其强大的功能和易用性,在生物信息学领域广受好评。UMI-tools 有非常详细的官方文档(网址:https://umi-tools.readthedocs.io/en/latest/),在里面可以找到详细的使用说明、参数解释和示例等,是学习和使用的首选资料。你也可以借助 Galaxy 生信云平台...
1写在前面上期我们分享了单细胞测序(scRNA-seq)的基本概念,样品的制备以及细胞的捕获。😁 本期我们继续介绍一下转录本定量分析、实验设计、批次效应和混杂... 2.6K40 RNAseq建库方法dtexternalnanasumi 生信喵实验柴 2022-10-25 当前RNAseq 主要研究的是 mRNA,由于一次转录过程中,mRNA 只占很少一部分(约 4~...
https://divingintogeneticsandgenomics.rbind.io/post/understand-10x-scrnaseq-and-scatac-fastqs/ Analysing 10X Single Cell RNASeq Data 10x的技术问题: How does Cell Ranger correct barcode sequencing errors? What is a barcode whitelist? 1 2
5.具有scRNA-seq和spatial transcriptomics 数据分析经验者,优先考虑。 福利待遇 基本工资按照NIH标准,医疗保险及退休金等各项福利待遇按照医学中心标准执行。 申请方式 请发送简历及个人情况简介至:zwang12@bidmc.harvard.edu 若想咨询以上留学相关信息,...