Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens

This repo contains Seurat objects, differential expression analysis results, and pathway gene lists for the manuscript "Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens"List of files: 1. Seurat_object_IFNB_Perturb_seq.rds: Seurat object of the Perturb-seq data for Interferon-beta pathway2. Seurat_object_IFNG_Perturb_seq.rds: Seurat object of the Perturb-seq data for Interferon-gamma pathway3. Seurat_object_TNFA_Perturb_seq.rds: Seurat object of the Perturb-seq data for TNF-alpha pathway4. Seurat_object_TGFB1_Perturb_seq.rds: Seurat object of the Perturb-seq data for TGF-beta1 pathway5. Seurat_object_INS_Perturb_seq.rds: Seurat object of the Perturb-seq data for insulin pathway6. Pathway_genelist.rds: The pathway gene lists from MultiCCA analysis7. Pathway_Exclusive_genelist.rds: The pathway exclusive gene lists generated from Pathway_genelist.rds8. HClust_Pathway_celltype_specific_genelist.rds: The cell-line specific pathway gene lists from hierarchical clustering analysis independently done on each cell line9. DE_results_all_pathway.zip: The DE test results for all the regulators, cell lines, and pathways (from Mixscale weighted DE test.)10. Bulk_RNAseq_Seurat_object_IFNG_and_TGFB_stim.rds: Seurat object for the bulk RNA-seq data for interferon-gamma and TGF-beta stimulation experiments11. Parse_Guide_Capture_Protocol.pdf: The guide RNA capture protocol developed for Parse Evercode Whole Transcriptome kit本仓库包含论文《基于可扩展单细胞扰动筛选的分子通路特征系统性重构》（原文标题："Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens"）配套的Seurat(Seurat)对象、差异表达分析结果以及通路基因集。文件列表如下： 1. Seurat_object_IFNB_Perturb_seq.rds：针对干扰素-β（Interferon-beta）通路的扰动测序（Perturb-seq）数据对应的Seurat对象 2. Seurat_object_IFNG_Perturb_seq.rds：针对干扰素-γ（Interferon-gamma）通路的扰动测序数据对应的Seurat对象 3. Seurat_object_TNFA_Perturb_seq.rds：针对肿瘤坏死因子-α（TNF-alpha）通路的扰动测序数据对应的Seurat对象 4. Seurat_object_TGFB1_Perturb_seq.rds：针对转化生长因子-β1（TGF-beta1）通路的扰动测序数据对应的Seurat对象 5. Seurat_object_INS_Perturb_seq.rds：针对胰岛素（insulin）通路的扰动测序数据对应的Seurat对象 6. Pathway_genelist.rds：来自多典型关联分析（MultiCCA）的通路基因集 7. Pathway_Exclusive_genelist.rds：由Pathway_genelist.rds生成的通路专属基因集 8. HClust_Pathway_celltype_specific_genelist.rds：对每个细胞系独立开展层级聚类分析后得到的细胞系特异性通路基因集 9. DE_results_all_pathway.zip：涵盖所有调控因子、细胞系及通路的差异表达（Differential Expression, DE）检验结果（基于Mixscale加权差异表达检验得到） 10. Bulk_RNAseq_Seurat_object_IFNG_and_TGFB_stim.rds：针对干扰素-γ与转化生长因子-β刺激实验的批量RNA测序（bulk RNA-seq）数据对应的Seurat对象 11. Parse_Guide_Capture_Protocol.pdf：为Parse Evercode 全转录组试剂盒开发的向导RNA捕获实验方案