lasseignelab/230926_EJ_Setbp1_AlternativeSplicing: Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1S858R Schinzel-Giedion Syndrome patient variant mouse

The 230926_EJ_Setbp1_AlternativeSplicing GitHub repository includes the following directories and files:

• bin/

• docker/

• Dockerfile: The original dockerfile used to build the initial docker image. Future images were pulled from this initial docker image. 

• Rstudio-prefs.json: JSON file with information on RStudio preferences.

• conda/

• environment.yml: Environment files used to build the Conda environment used for alignment with STAR Solo.

• data/: Contains all processed data generated during this project. The processed data is deposited on Zenodo (refer to the manuscript for details), which includes descriptions of all included files.

• doc/: Contains any files that were downloaded/accessed for this study.

• Data_Sheet_2.xlsx: AS gene list identified in human peripheral blood by Liu et al., 2022.

• G2MGenes.csv: cell cycle genes converted from human to mouse for Seurat pre-processing. Genes were converted on 240623.

• GOCC_SMALL_NUCLEAR_RIBONUCLEOPROTEIN_COMPLEX.v2023.2.Hs.tsv: List of known spliceosome components. Accessed on 240208

• README: README file for this subdirectory.

• SGenes.csv: ell cycle genes converted from human to mouse for Seurat pre-processing. Genes were converted on 240623.

• results/

• ambientRNA_removal/: includes rho density plots.

• as_gene_summaries/: includes publication-ready 3-panel figures for all significant SJU genes

• brain/: includes 33 significant SJU genes in the cerebral cortex

• kidney/: includes 62 significant SJU genes in the kidney

• distributions/: includes 5 PNGs of different gene, splice junction, and PSI score distributions in the cerebral cortex

• final_outputs/: includes all final figures. These can be accessed through the GitHub repository or seen in the paper.

• kidney_figures/: includes three kidney plots included in the manuscript.

• kidney_overview_figure.png

• setbp1.png

• setbp1_sj_expr_usage.png

• kidney_outputs/: includes gene and sj violin plots included as supplementary figure in the manuscript.

• genes_sjs_percell_violin.png

• marvel_outputs/: includes intermediate marvel outputs, primarily generated from the cerebral cortex data,

• seurat_outputs/: includes outputs generated during seurat preprocessing for the cerebral cortex and the kidney

• supplementary_figures/: includes supplementary figures included in the manuscript.

• tables/: includes tables that are referenced in the manuscript.

• upset_plots/: includes significant SJU gene UpSet plots in the cerebral cortex and the kidney

• README: subdirectory README file

• src/

• ambientRNA-removal/

• 01_ambientRNA_removal.R: ambient RNA removal at the gene count level of all samples.

• 01_ambientRNA_removal.sh: driver for 01_ambientRNA_removal.R

• figures/

• figure_2.Rmd: Code to make manuscript figure 2.

• figure_3-4.Rmd: Code to make manuscript figures 3 and 4.

• figure_5.Rmd: Code to make manuscript figure 5.

• functions.R: Functions script for figure scripts written by Emma F. Jones

• supp_figure_2.Rmd: Code to make manuscript supplementary figure 2.

• geom_split_violin.R: Code to make split violin plots

• mean_expression_celltype.R: Code to calculate cell-type-specific mean expression

• kidney_overview_figure.R: Code to make supplementary figure of kidney dataset overview.

• kidney_overview_figure.sh: Driver of kidney_overview_figure.R

• kidney_marvel_figures.R: Code to make MARVEL figures in the kidney data.

• Kidney_marvel_figures.sh: Driver of kidney_marvel_figures.R

• marvel/

• 01_format_MARVEL_data.Rmd: Code to format cerebral cortex MARVEL data

• 02_MARVEL_differential_analysis.Rmd: Code for differential MARVEL analysis in the cerebral cortex

• 03_analyze_de_genes.Rmd: DEA within MARVEL in the cerebral cortex

• 04_calc_sj_usage.Rmd: Splice junction usage analysis in the cerebral cortex

• 05_cell_specific_sj_expr.Rmd: Splice junction expression analysis in the cerebral cortex

• 06_format_kidney_MARVEL_data.R: Code to format kidney MARVEL data

• 06_format_kidney_MARVEL_data.sh: Driver of 06_format_kidney_MARVEL_data.R

• 07_kidney_MARVEL_differential_analysis.R: Code for differential MARVEL analysis in the kidney

• 07_kidney_MARVEL_differential_analysis.sh: Driver of 07_kidney_MARVEL_differential_analysis.R

• 08_analyze_kidney_de_genes.R: DEA within MARVEL in the kidney

• 08_analyze_kidney_de_genes.sh: Driver of 08_analyze_kidney_de_genes.R

• 09_calc_sj_usage_kidney.R: Splice junction usage analysis in the kidney

• 09_calc_sj_usage_kidney.sh: Driver of 09_calc_sj_usage_kidney.R

• 10_cell_specific_kidney_sj_expr.R: Splice junction expression analysis in the kidney

• 10_cell_specific_kidney_sj_expr.sh:  Driver of 10_cell_specific_kidney_sj_expr.R

• PlotSJPosition_modification.R: Modified MARVEL code to plot SJ position

• functions.R: MARVEL functions script written by Emma F. Jones

• samtools/: 

• sort_index_bam.sh: Code to sort the bam indices.

• seurat/

• 01_import_filter_data.Rmd: R Markdown for preprocessing cerebral cortex data

• 02_annotate_cell_types.Rmd: R Markdown for cell typing of the cerebral cortex data

• 03_kidney_preprocessing.R: Script for full Seurat preprocessing of the kidney data

• 03_kidney_preprocessing.sh: Driver of 03_kidney_preprocessing.R

• functions.R: Seurat-specific functions script written by Emma F. Jones

• generate_cellcycle_lists.R: R script to generate mouse cell cycle lists for Seurat quality control, written by Timothy C. Howton

• starsolo_conda/

• 01_build_STAR_genome.sh: Script for creating the STAR genome needed for alignment

• 02_run_STARsolo.sh: Script for running STAR Solo on all included samples.

• README: Subdirectory-specific README with STAR Solo instructions.

• README: source directory-specific README file

• functions_soelter.R: R script with functions for any code pertaining to manuscript revisions. Written and modified by Tabea M. Soelter.

• verifications/: includes multiple .md5 files that include script specific MD5sums used during verification in internal peer review

What's Changed

• Ambient rna removal by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/91
• Seurat processing after soupX by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/92
• Marvel re-analysis by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/93
• Brain DESeq2 Re-analysis by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/94
• Seurat pre-processing of the kidney S858R data by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/95
• Figure re-plotting for brain by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/96
• MARVEL analysis in kidney by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/97
• Kidney DESeq2 Analysis by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/98
• Kidney plotting by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/99
• Fix brain as summaries by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/100
• Clean repo by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/102
• Update readme by @tsoelter in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/101

New Contributors

• @tsoelter made their first contribution in https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/pull/91

Full Changelog: https://github.com/lasseignelab/230926_EJ_Setbp1_AlternativeSplicing/compare/1.0.0...2.0.0