Collection of supplementary materials for the paper "Clonal analysis of murine development reveals novel positional programs directing lineage progression"

This is the collection of supplementary materials for the paper “Clonal analysis of murine development reveals novel positional programs directing lineage progression” (Erickson et al.). All AnnData containers have normalized expressions stored in adata.X and raw counts stored in adata.layers["counts"]. In clone2vec AnnData objects fractions of the clone within the fate ([0; 1]) are stored in adata.X, and cell counts are stored in adata.layers["counts"]. This repository contains: Plasmids.zip — the archive with plasmids maps and additional sequences / CRISPR gRNAs descriptions that were used to build chimeric references, AnnDatas_Control_Trunk.zip — the archive with AnnData objects for control mice (trunk samples) — with all cells or with major domains of cells (neurons, mesenchyme, neural crest-derived, and others) + clonal embedding for all cells, AnnDatas_Control_Head.zip — the archive with AnnData objects for control mice (head samples) — with all cells or with major domains of cells (neurons, mesenchyme, and others) + clonal embedding for all cells, AnnDatas_Perturbed_Trunk.zip — the archive with AnnData objects for control and perturbed mice (trunk samples) — with all cells or with major domains of cells (neurons, mesenchyme, neural crest-derived, and others) + clonal embeddings for NC-derived cells and all cells, AnnDatas_Perturbed_Head.zip — the archive with AnnData objects for control and perturbed mice (head samples) — with all cells or with major domains of cells (neurons, mesenchyme, and others) + clonal embedding for all cells. AnnDatas_Lower_Trunk_NMP_NC.zip — the archive with AnnData objects for additionally sequenced control mice (lower trunk samples) — with all cells + clonal embedding for all cells. The code for the analysis is available on GitHub. Please, feel free to contact us if you need additional data: sergey.isaev[at]meduniwien.ac.at.本数据集为论文《小鼠发育的克隆分析揭示指导谱系进程的新型位置调控程序》（Erickson等人）的补充材料合集。 所有AnnData数据容器中，标准化后的表达矩阵存储于`adata.X`，原始计数矩阵存储于`adata.layers["counts"]`。在克隆向量化方法（clone2vec）相关的AnnData对象中，细胞克隆在命运中的占比（范围为[0; 1]）存储于`adata.X`，细胞计数则存储于`adata.layers["counts"]`。 本仓库包含以下内容： - Plasmids.zip：内含质粒图谱、用于构建嵌合参考序列的额外序列及CRISPR向导RNA（gRNAs）描述信息的压缩包； - AnnDatas_Control_Trunk.zip：内含对照小鼠躯干样本AnnData数据对象的压缩包，涵盖全部细胞或主要细胞类群（神经元、间充质细胞、神经嵴来源细胞及其他类群），并包含所有细胞的克隆嵌入特征； - AnnDatas_Control_Head.zip：内含对照小鼠头部样本AnnData数据对象的压缩包，涵盖全部细胞或主要细胞类群（神经元、间充质细胞及其他类群），并包含所有细胞的克隆嵌入特征； - AnnDatas_Perturbed_Trunk.zip：内含对照与扰动小鼠躯干样本AnnData数据对象的压缩包，涵盖全部细胞或主要细胞类群（神经元、间充质细胞、神经嵴来源细胞及其他类群），并包含神经嵴来源细胞与所有细胞的克隆嵌入特征； - AnnDatas_Perturbed_Head.zip：内含对照与扰动小鼠头部样本AnnData数据对象的压缩包，涵盖全部细胞或主要细胞类群（神经元、间充质细胞及其他类群），并包含所有细胞的克隆嵌入特征； - AnnDatas_Lower_Trunk_NMP_NC.zip：内含额外测序的对照小鼠下躯干样本AnnData数据对象的压缩包，涵盖全部细胞，并包含所有细胞的克隆嵌入特征。 本分析所用代码已托管至GitHub。若需获取额外数据，请联系我们：[e-mail]。