Code for the XDP ventral forebrain organoids manuscript

Find below a list of scripts and notebooks used to generate results (Figures and Tables) in the study entitled "A hexamer tandem repeat RNA embedded within an SVA retrotransposon drives R-loop formation and neurodegeneration." Each Figure or Table is accompanied by the link to relevant files in this repository.

Figure_or_Table	File_path
Figure 2B	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/_m/main.ipynb
Figure 2C	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/gsea/_m/main.ipynb
Figure 2C	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/gsea/filter_results/_m/main.ipynb
Figure 3B	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/expression_profiles/_m/main.ipynb
Figure 3C	xdp_striatal_organoids_35ratio_qpcr/analysis/report/_m/main.ipynb
Figure 4A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva_filter/_h/run
Figure 4A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva_filter/_h/process_sam.py
Figure 4A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva_filter/proper_pairs_overlapping_SVA_5prime/_m/main.ipynb
Figure 4A	xdp_hexamer_expression_viz/report_xdp_grant2023/_h/run.sh
Figure 4A	xdp_hexamer_expression_viz/report_xdp_grant2023/_m/report.ipynb
Figure 4B	xdp_5RACE_nanopore_sequencing_20240520_AL5RACE002/analysis/pod5/_h/run.sh
Figure 4B	xdp_5RACE_nanopore_sequencing_20240520_AL5RACE002/analysis/pod5/base_calling/_h/run.sh
Figure 4B	xdp_5RACE_nanopore_sequencing_20240520_AL5RACE002/analysis/pod5/base_calling/align/_h/run.sh
Figure 4B	xdp_5RACE_nanopore_sequencing_20240520_AL5RACE002/analysis/pod5/base_calling/align/report/_h/run.sh
Figure 4B	xdp_5RACE_nanopore_sequencing_20240520_AL5RACE002/analysis/pod5/base_calling/align/report/_m/report.ipynb
Figure 4B	xdp_5RACE_nanopore_sequencing_20240530_AL5RACE002/analysis/pod5/base_calling/align/report/_h/run.sh
Figure 4B	xdp_5RACE_nanopore_sequencing_20240530_AL5RACE002/analysis/pod5/base_calling/align/report/_m/report.ipynb
Figure 4B	xdp_5RACE_nanopore_sequencing_20240606_AL5RACE002/analysis/pod5/base_calling/align/report/_h/run.sh
Figure 4B	xdp_5RACE_nanopore_sequencing_20240606_AL5RACE002/analysis/pod5/base_calling/align/report/_m/report.ipynb
Figure 4D	sva_expression_brain_longr/download_data/_h/run.sh
Figure 4D	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Figure 4D	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Figure 4D	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Figure 4D	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/01_svas_and_coverage.ipynb
Figure 4D	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/02_sva_cats_and_enrichment.ipynb
Figure 4E	sva_expression_brain_longr/download_data/_h/run.sh
Figure 4E	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Figure 4E	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Figure 4E	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Figure 4E	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/02_sva_cats_and_enrichment.ipynb
Figure 5A	xdp_g4_pred/report/_h/run.sh
Figure 5A	xdp_g4_pred/report/_m/report.ipynb
Figure 5B	xdp_g4_pred/report/_h/run.sh
Figure 5B	xdp_g4_pred/report/_m/report.ipynb
Figure 5C	xdp_g4_pred/report/_h/run.sh
Figure 5C	xdp_g4_pred/report/_m/report.ipynb
Figure 5I	sva_expression_brain_longr/download_data/_h/run.sh
Figure 5I	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Figure 5I	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Figure 5I	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Figure 5I	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/02_sva_cats_and_enrichment.ipynb
Figure 6A	mann_whitney_xdp/_m/main.ipynb
Figure S1A	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_h/run.sh
Figure S1A	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_m/main.ipynb
Figure S1B	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_h/run.sh
Figure S1B	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_m/main.ipynb
Figure S1C	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_h/run.sh
Figure S1C	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_m/main.ipynb
Figure S1D	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_h/run.sh
Figure S1D	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/exploratory_analysis/_m/main.ipynb
Figure S1E	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/gsea/simplifyEnrichment/_h/run.sh
Figure S1E	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/gsea/simplifyEnrichment/_m/report.ipynb
Figure S2A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva/_h/run
Figure S2A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva/sort/_h/run
Figure S2A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva/sort/coverage/_h/run.sh
Figure S2A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva/sort/coverage/report/_h/run.sh
Figure S2A	xdp_striatal_organoids_RNA-seq/hisat2_with_xdp_sva/sort/coverage/report/_m/main.ipynb
Figure S3A	sva_expression_brain_longr/download_data/_h/run.sh
Figure S3A	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Figure S3A	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Figure S3A	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Figure S3A	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/02_sva_cats_and_enrichment.ipynb
Figure S4A	xdp_g4_pred/report/_h/run.sh
Figure S4A	xdp_g4_pred/report/_m/report.ipynb
Figure S4B	sva_expression_brain_longr/download_data/_h/run.sh
Figure S4B	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Figure S4B	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Figure S4B	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Figure S4B	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/02_sva_cats_and_enrichment.ipynb
Figure S4C	sva_expression_brain_longr/download_data/_h/run.sh
Figure S4C	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Figure S4C	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Figure S4C	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Figure S4C	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/02_sva_cats_and_enrichment.ipynb
Figure S6A	xdp_striatal_organoids_yh2ax/analysis/report/_h/run.sh
Figure S6A	xdp_striatal_organoids_yh2ax/analysis/report/_m/main.ipynb
Table S2	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/metadata/_m/main.ipynb
Table S2	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/metadata/metadata_formated_for_manuscript/_m/main.ipynb
Table S3	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/_m/main.ipynb
Table S4	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/gsea/_m/main.ipynb
Table S4	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_genes_no_lfcShrink_filter_low/gsea/filter_results/_m/main.ipynb
Table S5	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_exons_no_lfcShrink_filter_low/_m/main.ipynb
Table S5	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_exons_no_lfcShrink_filter_low/exons_expr_profile/_m/main.ipynb
Table S6	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_exons_no_lfcShrink_filter_low/_m/main.ipynb
Table S6	xdp_striatal_organoids_RNA-seq/analysis_speaqeasy/deseq2_multiplemodels_exons_no_lfcShrink_filter_low/exons_expr_profile/_m/main.ipynb
Table S7	sva_expression_brain_longr/download_data/_h/run.sh
Table S7	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Table S7	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Table S7	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Table S7	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/01_svas_and_coverage.ipynb
Table S8	sva_expression_brain_longr/download_data/_h/run.sh
Table S8	sva_expression_brain_longr/download_data/align/coverage_filtered/_h/run.sh
Table S8	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/_h/run.sh
Table S8	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_h/run.sh
Table S8	sva_expression_brain_longr/download_data/align/coverage_filtered/gen_matrices/plots/_m/02_sva_cats_and_enrichment.ipynb

Autobuild date: Wed Feb 26 02:44:49 PM EST 2025