DOI: 10.5281/zenodo.12535060
title: Data for Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1S858R Schinzel-Giedion Syndrome patient variant mouse

description: 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.tab