{"doi":"10.5281/zenodo.17594386","title":"Data for Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1S858R Schinzel-Giedion Syndrome patient variant mouse","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 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 ou","journal":"Zenodo (CERN European Organization for Nuclear Research)","year":2025,"id":586065,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10062,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9582,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":855742,"name":"Emma F. Jones","orcid":"0000-0003-4244-1456","position":1,"is_corresponding":false},{"id":1011804,"name":"Timothy C. Howton","orcid":"0000-0002-9423-0135","position":2,"is_corresponding":false},{"id":1500218,"name":"Crumley, Anthony B.","orcid":"0009-0004-7347-4722","position":3,"is_corresponding":false},{"id":1500219,"name":"Wilk, Elizabeth J.","orcid":"0000-0002-7078-1215","position":4,"is_corresponding":false},{"id":305258,"name":"Brittany N. Lasseigne","orcid":"0000-0002-1642-8904","position":5,"is_corresponding":false},{"id":817847,"name":"Tabea M. Soelter","orcid":"0000-0003-1654-4240","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:59:28.666390Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}