Data for Cell-type-specific alternative splicing in the cerebral cortex of a Schinzel-Giedion Syndrome patient variant mouse model
Author ORCID
Emma F. Jones 0000-0003-4244-1456
Timothy C. Howton 0000-0002-9423-0135
Tabea M. Soelter 0000-0003-1654-4240
Anthony B. Crumley 0009-0004-7347-4722
Brittany N. Lasseigne 0000-0002-1642-8904
Publication Date
6-25-2024
Abstract
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
Repository
Zenodo
Distribution License
Access Instructions and Link
This data is available under the MIT License
Funder
Funder: National Institutes of Health
Funder DOI: 10.13039/100000002
UAB Pilot Center for Precision Animal Modeling (C-PAM)
U54OD030167
