In summary, our data demonstrate the utility of large-scale TRAP screening to elucidate the cell type-specific gene expression changes that influence inflammation and wound healing. We identify the complement pathway as a whole, andc3a.1in particular, as significantly upregulated in neutrophils in ...
we generate in silico single-cell gene expression data for each cell type using BoolODE using the simulated GRNs and add 80% zeros in the simulation data. Then, we apply five multi-task learning algorithms and three single-task learning algorithms for GRN inference to ...
摘要 Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individualcellsof the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high-coverage single-cell RNA profiling, we asked whether long-term, h...
【3】Deal, R.B., and Henikoff, S. (2011). The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat. Protoc. 6, 56–68 【4】Phillips, J.E., and Corces, V.G. (2009). CTCF: master weaver of the genome. Cell 137, 1194–1211.论...
Cell type–specific genetic regulation of gene expression across human tissues GTEx项目已经确定了人体组织中大部分基因的顺式数量性状基因座(QTL)表达和剪接定量性状基因座。该研究绘制了细胞类型丰度和基因型的计算估计之间的相互作用,以确定七种细胞类型的细胞类型-相互作用QTL,并表明细胞类型相互作用表达QTL比组织...
2.然后,我们读取从[39]的Gene ExpressionOmnibus提交文件(NCBI Gene Expression Omni-bus,GSE97942)[39]下载的FC,VC和CB对应的各个数据矩阵。 这些存储在名为Data的本地可访问文件夹中。 由于这些表达矩阵的大多数条目均为“ 0”,因此我们立即使用Matrix程序包将它们转换为稀疏矩阵格式,以减少内存占用。
A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously estimates cell type-specific gene expression p
# Check expression of the three genes in the training set. sc.pl.violin(adata_2000, top_3_genes, groupby ='cell_type', rotation =90) mast_cell_weights = weights[model.cell_types =='Plasma cells'] top_3_genes = model.features[mast_cell_weights.argpartition(-3, axis =None)[-3:]]...
注:Single-cell atlas of gene expression and chromatin accessibility in the human intestine. A)Sections of the intestine from which cells were isolated for snRNA-seq and snATACseq 为了检查肠道区域之间的整体差异,我们首先将来自肠道所有区域的细胞聚集在一起,发现来自所有区域的免疫细胞和基质细胞聚集在一...
生物学重复的不同条件下的scrna-seq数据的差异基因表达分析 (https://www.10xgenomics.com/resources/analysis-guides/differential-gene-expression-analysis-in-scrna-seq-data-between-conditions-with-biological-replicates) 需要注意的是,这部分差异表达分析不应与下一部分,计算来自两个簇的细胞之间的差异表达基因以...