Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level

This collection of processed data accompanies the study: Yeh, Aguirre, Laveroni et al. Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level. (2024). Unpublished. This collection of processed data is purposed for easy access and computing directly in the R programming environment. All files are provided in the form of RObjects (extension .rds). Data collected and processed for the first time as a part of this study include: de-identified clinical annotations for a cohort of 94 patients diagnosed with tubo-ovarian high grade serous carcinoma (HGSC), morphology annotations from clinical images (Hematoxylin and Eosin), targeted genomic data, single cell spatial transcriptomics on 130 HGSC tumors, CRISPR-screen data in ovarian cancer cells in co-culture with T and Natural Killer (NK) cells, and Perturb-Seq data in ovarian cancer cells co-cultured with NK cells. Processed data from published journal articles include scRNA-Seq data downloaded from Synapse (syn33521743), Gene Expression Omnnibus (GSE118828, GSE173682, GSE147082, GSE154600, GSE146026). This following table provides a description of the files contained in this collection. File Object Type in R Description 01_MasterMetaData.rds data.frame Clinical annotations of patients in above study. 02_CNA.rds matrix Patient x Gene matrix of copy number alterations. 03_Discovery_data.rds list Single cell spatial transcriptomics data collected on CosMx Single Molecule Imaging Platform (Discovery Dataset). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 04_Validation1_data.rds list Single cell spatial transcriptomics data collected on 10X Xenium Platform (Validation Dataset 1). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 05_Validation2_data.rds list Single cell spatial transcriptomics data collected on Vizgen's Multiplexed Error Robust Fluorescent in situ Hybridization Platform (Validation Dataset 2). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 06_Test1_data.rds list Single cell spatial transcriptomics data collected on CosMx Single Molecule Imaging Platform (Test 1 Dataset). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 07_Test2_SMIWT_1_data.rds list Single cell spatial transcriptomics data collected on CosMx Single Molecule Imaging Platform (Test 2 Dataset, Patient HGSC1). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 08_Test2_SMIWT_2_data.rds list Single cell spatial transcriptomics data collected on CosMx Single Molecule Imaging Platform (Test 2 Dataset, Patient HGSC2). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 09_Test2_SMIWT_8_data.rds list Single cell spatial transcriptomics data collected on CosMx Single Molecule Imaging Platform (Test 2 Dataset, Patient HGSC8). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 10_Test2_SMIWT_113_data.rds list Single cell spatial transcriptomics data collected on CosMx Single Molecule Imaging Platform (Test 2 Dataset, Patient HGSC113). This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level including cell.types is stored in this list. 11_scRNA_Geistliner_r.rds list Single cell RNA-Seq data downloaded from GEO (GSE154600), processed to match the data structure of the spatial transcriptomics data described for 04_SMI_data.rds, 05_Xenium_data.rds, 06_MERFISH_data.rds. 12_scRNA_Olalekan_r.rds list Single cell RNA-Seq data downloaded from GEO (GSE147082), processed to match the data structure of the spatial transcriptomics data described for 04_SMI_data.rds, 05_Xenium_data.rds, 06_MERFISH_data.rds. 13_scRNA_Qian_r.rds list Single cell RNA-Seq data downloaded from https://lambrechtslab.sites.vib.be/en/data-access, processed to match the data structure of the spatial transcriptomics data described for 04_SMI_data.rds, 05_Xenium_data.rds, 06_MERFISH_data.rds. 14_scRNA_Regner_r.rds list Single cell RNA-Seq data downloaded from GEO (GSE173682), processed to match the data structure of the spatial transcriptomics data described for 04_SMI_data.rds, 05_Xenium_data.rds, 06_MERFISH_data.rds. 15_scRNA_Shih_r.rds list Single cell RNA-Seq data downloaded from GEO (GSE118828), processed to match the data structure of the spatial transcriptomics data described for 04_SMI_data.rds, 05_Xenium_data.rds, 06_MERFISH_data.rds. 16_scRNA_VazquezGarcia_r.rds list Single cell RNA-Seq data downloaded from Synapse (syn33521743), processed to match the data structure of the spatial transcriptomics data described for 04_SMI_data.rds, 05_Xenium_data.rds, 06_MERFISH_data.rds. 17_StromalMorphology.rds data.frame Tissue morphology annotations made by a board-certified gynecological pathologist of each sample in the SMI (Discovery) dataset 18_CRISPR.rds data.frame Z-scores of ovarian cancer cell line resistance to T and NK cell mediated killing based as a function of genetic perturbations via CRISPR. 19_PerturbSeq_TYKnuNK.rds list Perturb-Seq data of ovarian cancer cells under co-culture with NK cells. This list contains the raw counts data in the field "cd" and transcripts per million data in "tpm". All meta data on the cell-level is stored in this list.