Single-cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches – Source data 2 relative to Figs 3-5, S2-S8

.rds files for Chromium (Fig. 3, 5, S2-4, S7) and MARS-seq (Fig. 4, 5, S6, 8) datasets (plus the integrated Chromium / MARS-seq dataset, Fig. S5). The rds files contains only final the analyzed cells, used for all plotting and analysis (all low-quality cells and contaminant cells (see Methods) have been removed). For more detailed description of cells used for both sc-RNA-seq, see respective Method paragraphs. Each .rds file contains metadata that can be used to subset datasets by replicate, region, transgenic origin, cell types, phase… Only the datasets generated in the lab are made available in this repository. The 3 R scripts contain the codes used for the plotting of all figures. Sc-RNA-seq plots are in majority made using Seurat package functions. Additional plots are made with ggstatplots package or ggplot package and extensions. All library used are listed at the top of the scripts. The source data table file, classified with a unique tab for each figure panel, contains the data used conjointly with the .rds files to generate all plots using the aforementionned scripts.本数据集包含用于绘制图3、5、S2-4、S7的Chromium（Chromium）平台测序数据集，以及用于绘制图4、5、S6、8的MARS-seq（MARS-seq）数据集，此外还包含整合后的Chromium与MARS-seq联合数据集（对应图S5）。上述.rds（.rds）文件仅收录经最终分析的细胞，所有绘图与分析均基于该数据集开展，所有低质量细胞及污染细胞（详见方法部分）均已被剔除。若需了解两种单细胞RNA测序（sc-RNA-seq，single-cell RNA sequencing）所用细胞的详细信息，请参阅对应方法章节。每个.rds 文件均包含元数据，可依据重复实验、样本区域、转基因起源、细胞类型、细胞周期时相等条件对数据集进行子集划分。本仓库仅公开本实验室生成的数据集。 本仓库包含3个R脚本，内含用于绘制所有图片的代码。其中绝大多数单细胞RNA测序绘图均基于Seurat（Seurat）包的函数完成，其余绘图则使用ggstatplots（ggstatplots）包或ggplot（ggplot）包及其拓展工具完成。本脚本顶部已列出所有依赖的工具库。 本仓库附带源数据表文件，该文件为每个图片面板设置了独立工作表，其中收录的数据可与上述.rds 文件配合，通过前文提及的脚本完成所有绘图工作。