Data for Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1S858R Schinzel-Giedion Syndrome patient variant mouse

data.tar.gz contains all files from the data directory (except for sam outputs from STAR) associated with the 230926_EJ_Setbp1_AlternativeSplicing GitHub project and includes the following files: ./marvel: This directory contains rds and Rdata objects that were created using the MARVEL R package cell_type_goresults.rds: This is the go results split by cell type in the cerebral cortex. gene_counts_kidney.rds: The object includes the gene counts in the kidney. marvel_04_split_counts.Rdata: This R data includes all environment objects from MARVEL script 04, and is used for downstream plotting in the cerebral cortex normalized_kidney_sj_expression.Rds: This object is the normalized splice junction expression in the kidney normalized_sj_expression.Rds: This object is the normalized splice junction expression in the cerebral cortex setbp1_kidney_marvel_aligned.rds: Final prepared MARVEL object before any SJU analyses have been run in the kidney setbp1_marvel_aligned.rds: Final prepared MARVEL object before any SJU analyses have been run in the cerebral cortex significant_tables_kidney.RData: For those who do not want to load multiple massive files, this includes all significant SJU results for each cell type in the kidney significant_tables.RData: For those who do not want to load multiple massive files, this includes all significant SJU results for each cell type in the cerebral cortex sj_counts_kidney.rds: Splice junction counts in the kidney. sj_usage_cell_type.rds: This data object has splice junction usage calculated for each cell type in the cerebral cortex sj_usage_condition.rds: This data object has splice junction usage calculated for each cell type and also split by condition in the cerebral cortex sj_usage_kidney_cell_type.rds: This data object has splice junction usage calculated for each cell type in the kidney sj_usage_kidney_condition.rds: This data object has splice junction usage calculated for each cell type and also split by condition in the kidney split_matrices_list_kidney.rds: Lists of split MARVEL matrices in the kidney ./seurat: - This directory contains all intermediate and final Seurat single-cell gene expression objects annotated_brain_samples.rds: This is the final iteration of the processing in Seurat for a final annotated object. Please use this object for any Seurat or single-cell gene expression analyses. clustered_brain_samples.rds: This is the clustered Seurat object, before cell type annotation based on canonical markers. filtered_brain_samples_pca.rds: This is the filtered Seurat object, before clustering but after PCA. filtered_brain_samples.rds: This is the filtered Seurat object, before PCA. integrated_brain_samples.rds: This is the integrated Seurat object, before other steps. annotated_kidney_samples.rds: This is the final iteration of the processing in Seurat for a final annotated object. Please use this object for any Seurat or single-cell gene expression analyses. clustered_kidney_samples.rds: This is the clustered Seurat object, before cell type annotation based on canonical markers. filtered_kidney_samples_pca.rds: This is the filtered Seurat object, before clustering but after PCA. filtered_kidney_samples.rds: This is the filtered Seurat object, before PCA. integrated_kidney_samples.rds: This is the integrated Seurat object, before other steps. ./soupX: - This directory contains all final SoupX corrected files by sample. We show the data structure using sample J1 only, as all directories mimic it. J1/: This directory contains outputs for brain sample J1 barcodes.tsv: SoupX corrected barcode file genes.tsv: SoupX corrected genes file matrix.mtx: SoupX corrected matrix file J13/: This directory contains outputs for brain sample J13 J15/: This directory contains outputs for brain sample J15 J2/: This directory contains outputs for brain sample J2 J3/: This directory contains outputs for brain sample J3 J4/: This directory contains outputs for brain sample J4 K1/: This directory contains outputs for kidney sample K1 K2/: This directory contains outputs for kidney sample K2 K3/: This directory contains outputs for kidney sample K3 K4/: This directory contains outputs for kidney sample K4 K5/: This directory contains outputs for kidney sample K5 K6/: This directory contains outputs for kidney sample K6 ./star: - All files in the STAR directory are outputs from STARsolo, as described in our methods. Each output directory contains the same files, so only one example is included here for brevity. Intermediate SAM files were removed to optimize space. J1/: This directory contains outputs for brain sample J1 Log.final.out Log.out Log.progress.out SJ.out.tab Solo.out/ Barcodes.stats GeneFull_Ex50pAS/: This directory contains the filtered and raw barcodes, features, and matrix files for gene expression (including introns) Features.stats filtered/ barcodes.tsv.gz: This file contains filtered cell barcodes features.tsv.gz: This file contains filtered features (genes) matrix.mtx.gz: This file contains the filtered cell by gene expression count matrix raw/ barcodes.tsv features.tsv matrix.mtx Summary.csv UMIperCellSorted.txt SJ/: This directory contains the QC and raw barcodes, features, and matrix files for splice junction expression Features.stats raw/: This directory contains the raw barcodes, features, and matrix files for splice junction expression barcodes.tsv: This file contains filtered cell barcodes features.tsv: This file contains filtered features (splice junctions) matrix.mtx: This file contains the filtered cell by gene expression count matrix Summary.csv STARgenome/: This directory contains the STARgenome created and used by STAR for this sample. Detailed file descriptions available from https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf exonGeTrInfo.tab exonInfo.tab geneInfo.tab sjdbInfo.txt sjdbList.fromGTF.out.tab sjdbList.out.tab transcriptInfo.tab J13/: This directory contains outputs for brain sample J13 J15/: This directory contains outputs for brain sample J15 J2/: This directory contains outputs for brain sample J2 J3/: This directory contains outputs for brain sample J3 J4/: This directory contains outputs for brain sample J4 K1/: This directory contains outputs for kidney sample K1 K2/: This directory contains outputs for kidney sample K2 K3/: This directory contains outputs for kidney sample K3 K4/: This directory contains outputs for kidney sample K4 K5/: This directory contains outputs for kidney sample K5 K6/: This directory contains outputs for kidney sample K6 genome/: This directory contains outputs from running STAR genomeGenerate. Detailed file descriptions available from https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf chrLength.txt chrNameLength.txt chrName.txt chrStart.txt exonGeTrInfo.tab exonInfo.tab geneInfo.tab Genome genomeParameters.txt Log.out SA SAindex sjdbInfo.txt sjdbList.fromGTF.out.tab sjdbList.out.tab transcriptInfo.tabdata.tar.gz 包含了与230926_EJ_Setbp1_AlternativeSplicing GitHub项目相关的data目录下的所有文件（STAR生成的SAM（Sequence Alignment/Map，序列比对映射）输出文件除外），并包含以下文件： ./marvel：该目录包含使用MARVEL R包（MARVEL R package）创建的rds与Rdata格式对象 cell_type_goresults.rds：该文件存储大脑皮层中按细胞类型拆分的GO（Gene Ontology，基因本体）分析结果 gene_counts_kidney.rds：该对象存储肾脏组织中的基因计数数据 marvel_04_split_counts.Rdata：该R数据对象包含MARVEL脚本04的所有环境对象，用于大脑皮层的后续可视化分析 normalized_kidney_sj_expression.Rds：该对象存储肾脏组织中经标准化处理的剪接接头（splice junction, SJ）表达量数据 normalized_sj_expression.Rds：该对象存储大脑皮层中经标准化处理的剪接接头表达量数据 setbp1_kidney_marvel_aligned.rds：肾脏组织中未开展任何剪接接头使用（splice junction usage, SJU）分析前的最终预处理MARVEL对象 setbp1_marvel_aligned.rds：大脑皮层中未开展任何剪接接头使用分析前的最终预处理MARVEL对象 significant_tables_kidney.RData：针对不愿加载多个大文件的用户，该文件存储肾脏组织中各细胞类型的所有显著SJU分析结果 significant_tables.RData：针对不愿加载多个大文件的用户，该文件存储大脑皮层中各细胞类型的所有显著SJU分析结果 sj_counts_kidney.rds：肾脏组织中的剪接接头计数数据 sj_usage_cell_type.rds：该数据对象存储大脑皮层中各细胞类型的剪接接头使用量计算结果 sj_usage_condition.rds：该数据对象存储大脑皮层中各细胞类型且按实验条件拆分的剪接接头使用量计算结果 sj_usage_kidney_cell_type.rds：该数据对象存储肾脏组织中各细胞类型的剪接接头使用量计算结果 sj_usage_kidney_condition.rds：该数据对象存储肾脏组织中各细胞类型且按实验条件拆分的剪接接头使用量计算结果 split_matrices_list_kidney.rds：肾脏组织中拆分后的MARVEL矩阵列表 ./seurat：该目录包含所有中间与最终的Seurat单细胞基因表达对象 annotated_brain_samples.rds：大脑样本Seurat处理的最终版本，为完成注释的对象。请使用该对象开展所有Seurat或单细胞基因表达分析 clustered_brain_samples.rds：基于经典标记物进行细胞类型注释前的已聚类Seurat对象 filtered_brain_samples_pca.rds：完成聚类前但已完成主成分分析（principal component analysis, PCA）的过滤后Seurat对象 filtered_brain_samples.rds：完成主成分分析前的过滤后Seurat对象 integrated_brain_samples.rds：完成其他分析步骤前的已整合Seurat对象 annotated_kidney_samples.rds：肾脏样本Seurat处理的最终版本，为完成注释的对象。请使用该对象开展所有Seurat或单细胞基因表达分析 clustered_kidney_samples.rds：基于经典标记物进行细胞类型注释前的已聚类Seurat对象 filtered_kidney_samples_pca.rds：完成聚类前但已完成主成分分析的过滤后Seurat对象 filtered_kidney_samples.rds：完成主成分分析前的过滤后Seurat对象 integrated_kidney_samples.rds：完成其他分析步骤前的已整合Seurat对象 ./soupX：该目录包含所有经SoupX校正的单样本最终文件。本次仅以样本J1为例展示数据结构，其余目录结构与之完全一致 J1/：该目录包含大脑样本J1的分析输出 barcodes.tsv：经SoupX校正的条形码文件 genes.tsv：经SoupX校正的基因文件 matrix.mtx：经SoupX校正的矩阵文件 J13/：该目录包含大脑样本J13的分析输出 J15/：该目录包含大脑样本J15的分析输出 J2/：该目录包含大脑样本J2的分析输出 J3/：该目录包含大脑样本J3的分析输出 J4/：该目录包含大脑样本J4的分析输出 K1/：该目录包含肾脏样本K1的分析输出 K2/：该目录包含肾脏样本K2的分析输出 K3/：该目录包含肾脏样本K3的分析输出 K4/：该目录包含肾脏样本K4的分析输出 K5/：该目录包含肾脏样本K5的分析输出 K6/：该目录包含肾脏样本K6的分析输出 ./star：该目录下的所有文件均为STARsolo的分析输出，详见本文方法部分。所有输出目录的文件结构一致，为精简篇幅，本次仅展示一个示例目录。为优化存储空间，已移除中间SAM文件 J1/：该目录包含大脑样本J1的分析输出 Log.final.out Log.out Log.progress.out SJ.out.tab Solo.out/ Barcodes.stats GeneFull_Ex50pAS/：该目录包含基因表达（含内含子区域）的过滤后与原始条形码、特征及矩阵文件 Features.stats filtered/ barcodes.tsv.gz：该文件存储过滤后的细胞条形码 features.tsv.gz：该文件存储过滤后的特征（基因） matrix.mtx.gz：该文件存储过滤后的细胞-基因表达计数矩阵 raw/ barcodes.tsv features.tsv matrix.mtx Summary.csv UMIperCellSorted.txt SJ/：该目录包含剪接接头表达的质控与原始条形码、特征及矩阵文件 Features.stats raw/：该目录包含剪接接头表达的原始条形码、特征及矩阵文件 barcodes.tsv：该文件存储过滤后的细胞条形码 features.tsv：该文件存储过滤后的特征（剪接接头） matrix.mtx：该文件存储过滤后的细胞-基因表达计数矩阵 Summary.csv STARgenome/：该目录包含STAR为该样本创建并使用的STAR基因组文件，详细文件说明可参考https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf exonGeTrInfo.tab exonInfo.tab geneInfo.tab sjdbInfo.txt sjdbList.fromGTF.out.tab sjdbList.out.tab transcriptInfo.tab J13/：该目录包含大脑样本J13的分析输出 J15/：该目录包含大脑样本J15的分析输出 J2/：该目录包含大脑样本J2的分析输出 J3/：该目录包含大脑样本J3的分析输出 J4/：该目录包含大脑样本J4的分析输出 K1/：该目录包含肾脏样本K1的分析输出 K2/：该目录包含肾脏样本K2的分析输出 K3/：该目录包含肾脏样本K3的分析输出 K4/：该目录包含肾脏样本K4的分析输出 K5/：该目录包含肾脏样本K5的分析输出 K6/：该目录包含肾脏样本K6的分析输出 genome/：该目录包含运行STAR genomeGenerate的输出结果，详细文件说明可参考https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf chrLength.txt chrNameLength.txt chrName.txt chrStart.txt exonGeTrInfo.tab exonInfo.tab geneInfo.tab Genome genomeParameters.txt Log.out SA SAindex sjdbInfo.txt sjdbList.fromGTF.out.tab sjdbList.out.tab transcriptInfo.tab