DOI: 10.5281/zenodo.12535061
title: Data for Cell-type-specific alternative splicing in the cerebral cortex of a Schinzel-Giedion Syndrome patient variant mouse model

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

marvel_04_split_counts.Rdata - This R data includes all environment objects from MARVEL script 04, and is used for downstream plotting

normalized_sj_expression.Rds - This object is the normalized splice junction expression

Setbp1_marvel_aligned.rds - Final prepared MARVEL object before any SJU analyses have been run

significant_tables.RData - For those who do not want to load multiple massive files, this includes all significant SJU results for each cell type

sj_usage_cell_type.rds - This data object has splice junction usage calculated for each cell type

sj_usage_condition.rds - This data object has splice junction usage calculated for each cell type and also split by condition

 

./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 the integrated Seurat object, before other steps.

 

./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

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/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

 

./star/J1: - This is the head STAR directory for sample J1. It contains logs, basic QC, and gene and splice junction counts. For more information about the STAR pipeline and its outputs, please refer to the STAR documentation https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf 

Log.final.out

Log.out

Log.progress.out

SJ.out.tab

Solo.out/

STARgenome/

 

./star/J1/Solo.out:- This directory contains the outputs used for downstream analysis

Barcodes.stats

GeneFull_Ex50pAS/

SJ/

 

./star/J1/Solo.out/GeneFull_Ex50pAS: - This directory contains the filtered and raw barcodes, features, and matrix files for gene expression (including introns)

Features.stats

filtered/

raw/

Summary.csv

UMIperCellSorted.txt

 

./star/J1/Solo.out/GeneFull_Ex50pAS/filtered: - This directory contains the filtered tsv and mtx gene expression files required for creating a Seurat object (or other single cell packages)

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

 

./star/J1/Solo.out/GeneFull_Ex50pAS/raw: - This directory contains the unfiltered tsv and mtx gene expression files required for creating a Seurat object (or other single cell packages). Files are the same as previously described for filtered.

barcodes.tsv

features.tsv

matrix.mtx

 

./star/J1/Solo.out/SJ: - This directory contains the QC and raw barcodes, features, and matrix files for splice junction expression

Features.stats

raw/

Summary.csv

 

./star/J1/Solo.out/SJ/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

 

./star/J1/_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