Mapping spatial organization in ovarian cancer uncovers drivers of immune evasion
Creators
- 1. Stanford University School of Medicine, Department of Biomedical Data Science
- 2. Stanford University School of Medicine, Cancer Biology Program
- 3. Stanford University School of Medicine, Department of Genetics
- 4. Stanford University School of Medicine, Department of Pathology
- 5. California Pacific Medical Center, Department of Pathology
Description
This collection of processed data accompanies the study: Yeh, Aguirre, Laveroni et al. Mapping spatial organization in ovarian cancer uncovers drivers of immune evasion. (2023). Unpublished.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 60 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 95 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_Clinical.rds | data.frame | Clinical annotations of patients in above study. |
| 02_ClinicalDataColumnKey.rds | data.frame | Key for Column IDs in 01_Clinical.rds |
| 03_CNA.rds | matrix | Patient x Gene matrix of copy number alterations. |
| 04_SMI_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. |
| 05_Xenium_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. |
| 06_MERFISH_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. |
| 07_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. |
| 08_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. |
| 09_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. |
| 10_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. |
| 11_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. |
| 12_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. |
| 13_StromalMorphology.rds | data.frame | Tissue morphology annotations made by a board-certified gynecological pathologist of each sample in the SMI (Discovery) dataset |
| 14_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. |
| 15_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. |
Files
Restricted
The record is publicly accessible, but files are restricted to users with access.
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This data is currently not available in the public domain and is only available to reviewers of our manuscript: Yeh, Aguirre, Laveroni et al. Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level. (2024). The private link to this collection on Zenodo should have been provided to reviewers through the journal's editorial office.
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