b.选中2列log2fc结果,用excel绘制散点图,添加趋势线(可以显示公式和R平方)。 [1]Chen X, Yang X, Xie J, Ding W, Li Y, Yue Y, Wang L. Biochemical and Comparative Transcriptome Analyses Reveal Key Genes Involved in Major Metabolic Regulation Related to Colored Leaf Formation in Osmanthus fragra...
RunType:声明数据处理级别,一般只用到两个,stddata代表level3,analyses代表level4 Date:数据在firehose中的处理日期,一般都用最新的,latest [disease_cohort, ...]:声明要下载的癌症类型,诸如acc,blca等等 简言之,就是啥数据,啥级别,啥日子,啥肿瘤,多写几遍就OK了。 数据至此就下载完了,接下来的活就要在R中...
选择的内参基因在不同样品里是否稳定表达,是另一个影响qPCR相对定量结果的关键因素。 6、两种技术本身存在差异: 转录组测序是基于检测样品里所有基因整体上的表达情况,qPCR是特异性设计引物对基因的局部区域做相对定量的,两者的技术原理是存在一定不同的,所以转录组和qPCR确实有可能存在并没有非常一致的情况的,一般来...
【4】Luo Y, Coskun V, Liang A et al. Single-cell transcriptome analyses reveal signals to activate dormant neural stem cells. Cell, 2015, 161: 1175–1186. 【5】Meng J, Zhu Q, Zhang L et al. Genome and transcriptome analyses provide insight into the euryhaline adaptation mechanism of Cras...
b.选中2列log2fc结果,用excel绘制散点图,添加趋势线(可以显示公式和R平方)。 [1]Chen X, Yang X, Xie J, Ding W, Li Y, Yue Y, Wang L. Biochemical and Comparative Transcriptome Analyses Reveal Key Genes Involved in Major Metabolic Regulation Related to Colored Leaf Formation in Osmanthus fragra...
paper: The impact of amplification on differential expression analyses by RNA-seqComputational removal of read duplicates is not recommended for differential expression analysis. paper: Normalization of RNA-seq data using factor analysis of control genes or samples: About spike-ins control and R normali...
Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce...
MCF-7 is one of the most commonly used breast cancer cell lines. We used both short-read and long-read data for this sample in our analyses. Illumina MiSeq/HiSeq sequencing. Prior to sequencing, the MCF7 total RNA was assessed for fragmentation and quality using Agilent Bioanalysis and Qub...
bioconductor: using scran to perform basic analyses of single-cell RNA-seq data scater: single-cell analysis toolkit for expression with R Monovar: single-nucleotide variant detection in single cells paper: Comparison of methods to detect differentially expressed genes between single-cell populationssingl...
sc_analyses.png scRNA-seq分析面临的挑战 在scRNA-seq之前,使用大量RNA-seq进行转录组分析,这是一种比较细胞表达平均值的简单方法。如果寻找疾病生物标志物,或者不期望或不关心样品中的大量细胞异质性,则这可能是最佳方法。 尽管大量RNA-seq可以探索不同条件(例如治疗或疾病)之间基因表达的差异,但无法充分捕获细胞水...