Multiplexed single-cell characterization of alternative polyadenylation regulators (HEK293FT & K562 Perturb-seq data)
收藏资源简介：
This site provides access to datasets from the CPA-Perturb-seq manuscript Kowalski*, Wessels*, Linder* et al., including processed Perturb-seq datasets from HEK293FT and K562. We release these data as Seurat objects, where each object contains single-cell quantifications of gene expression (RNA assay), and in addition, quantifications of polyA site usage (polyA site assay). To explore these data, please install the PASTA (PolyA Site analysis using relative Transcript Abundance) package, which provides infrastructure and analytical tools to explore alternative polyadenylation at single-cell resolution. For each dataset, we also include a fragment file which enables visualization of read coverage plots across groups of cells. The files include: 1. CPA_K562.Rds : Seurat object containing the K562 CPA-Perturb-seq dataset 2. CPA_K562_fragments.tsv.gz : Fragment file for the K562 dataset 3. CPA_K562_fragments.tsv.gz.tbi : Fragment file index for the K562 dataset R code below: library(PASTA) k562 <- readRDS("CPA_K562.Rds") # Add fragments for plotting Fragments(k562) <- CreateFragmentObject(path = "download/CPA_K562_blocks.tsv.gz", cells = Cells(k562)) # visualize polyA site usage PolyACoveragePlot(k562, region ="chr7-26212195-26213351")
本站点提供由Kowalski*、Wessels*、Linder*等人发表的CPA-Perturb-seq研究手稿配套数据集的访问权限，其中包含HEK293FT与K562细胞系的经预处理Perturb-seq数据集。我们以Seurat对象形式发布上述数据：每个对象均包含基因表达的单细胞定量结果（RNA检测实验），同时还附带多聚腺苷酸位点使用情况的定量数据（polyA位点检测实验）。若需探索此类数据，请安装PASTA（基于相对转录本丰度的多聚腺苷酸位点分析工具包，PolyA Site analysis using relative Transcript Abundance），该工具包提供了用于在单细胞分辨率下探究可变多聚腺苷酸化现象的基础设施与分析工具。针对每个数据集，我们还提供了片段文件，支持对细胞组的读取覆盖度绘图进行可视化。 提供的文件如下： 1. CPA_K562.Rds：包含K562细胞系CPA-Perturb-seq数据集的Seurat对象 2. CPA_K562_fragments.tsv.gz：K562数据集的片段文件 3. CPA_K562_fragments.tsv.gz.tbi：K562数据集的片段文件索引 以下为示例R代码： r library(PASTA) k562 <- readRDS("CPA_K562.Rds") # 添加上传绘图所需的片段文件 Fragments(k562) <- CreateFragmentObject(path = "download/CPA_K562_blocks.tsv.gz", cells = Cells(k562)) # 可视化多聚腺苷酸位点使用情况 PolyACoveragePlot(k562, region ="chr7-26212195-26213351")
