Thanks to innovative sample-preparation and sequencing technologies, gene expression in individual cells can now be measured for thousands of cells in a single experiment. Since its introduction, single-cell RNA sequencing (scRNA-seq) approaches have rev
A step-by-step workflow for low-level analysis of single-cell RNA-seq data [version 1; referees: 5 approved with reservations]2016.Lun, A.T.; McCarthy, D.J.; Marioni, J.C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res 2016...
NCBI下载SRA数据有四种方法: NCBI官方的 SRA Toolkit 进行下载 aspera 工具下载 wget, curl 命令直接下载 grabseqs 工具下载 一、 NCBI官方的 SRA Toolkit 进行下载1. 首先需要获取这个项目的编号,在SRA数据库…
Single-cell RNA-sequencing (scRNA-seq) technology provides an excellent platform for measuring the expression profiles of genes in heterogeneous cell populations. Multiple tools for the analysis of scRNA-seq data have been developed over the years. The tools require complicated commands and steps to...
On the other side, keep in mind that pseudo-mapping will not be suitable for applications where the full alignment is needed (e.g. variant calling from RNA-seq data). Another example of the differences in the downstream analysis steps and the required tools across sequencing-based application ...
qPCR enables analysis of target protein–DNA complex levels in different experimental conditions. Figure 2 shows enrichment of histone H2A-Ub by ChIP, where the purified DNA was first analyzed by qPCR for the presence of specific promoter regio...
DNA微阵列: 将RNA打碎,用基于reference的探针(特指基因芯片)测得序列,此方法灵敏性高 RNA-seq:将RNA打碎,再将片段RNA反转录cDNA,利用二代测序(short reads)assembly而成。 Long noncoding RNA 定义: 1.因为200bp,所以long; 2.因为No protein produce但同时有与coding gene具有相似结构(都有intro和exon),所以ln...
{ # 把 1:n 按照每份 by 个分组,每个编号前后都不在一组,见接下来的例子 merge.indices <- lapply( X = 1:length(x = split.cells), FUN = seq.int, to = length(x = object), by = length(x = split.cells) ) # lapply( # X = 1:3, # FUN = seq.int, # to = 20, # by = ...
The analysis was performed using G. uralensis RNA-seq transcriptome data from different tissues. The co-expression network was visualized by Cytoscape. Homologous plant ApiGT genes were searched using online transcriptome data via China National GeneBank (https://db.cngb.org/blast/) which contains ...
This method can be used with different types of RNA, including mRNAs, lncRNAs, and circRNAs. There are several variations of CLIP, including: Crosslinking and Immunoprecipitation of RNA-Binding Proteins (CLIP-seq): This method is used to study the RNA binding sites of a protein by immuno...