ovary_geomx study

public/ovary_geomx_gray_foundation_2024/README.md

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+# Data transformation of ovary_geomx_gray_foundation_2024
+
+Article: Tanjina et al. bioRxiv 2024. https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-24-1366/750608/Multimodal-Spatial-Profiling-Reveals-Immune
+
+Data was downloaded from the supplementary files:
+- Table S1 and Table S2: Patient and Sample clinical data.
+
+
+## Notes on data transformation
+
+**Metadata**
+- Clinical data was inferred from the supplementary table S1 and S2. 
+- Manual distinction was made on patient and sample attributes.
+
+**Expression data**
+
+_mRNA_
+
+- RNA seq expression levels obtained from GeOmx were inferred from the table S8, sheet.
+- Gene expression data for spatially resolved regions (tumor, immune, stromal compartments).
+
+**Cell_type_fractions**
+
+- Counts of immune and stromal cells were normalized per ROI area (e.g., cells/mm²).
+- Data was shared by the author.
+- Transformed as generic assay
+
+**Cell_intensity**
+
+- Intensity of P53 was measured in Relative Fluorescence Units (RFU), a standardized method for quantifying fluorescence-based protein expression levels.
+- Data was shared by the author.
+- Transformed as generic assay

public/ovary_geomx_gray_foundation_2024/case_lists/cases_all.txt

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+case_list_category: all_cases_in_study
+stable_id: ovary_geomx_gray_foundation_2024_all
+case_list_name: All samples
+case_list_description: All tumor samples
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+case_list_ids: LSP16160_Scan2-024-Full-ROI	LSP16160_Scan2-023-Full-ROI	LSP16160_Scan2-022-Full-ROI	LSP16160_Scan2-021-Full-ROI	LSP16160_Scan2-020-Full-ROI	LSP16160_Scan2-019-Full-ROI	LSP16160_Scan2-018-Full-ROI	LSP16160_Scan2-017-Full-ROI	LSP16160_Scan2-016-Full-ROI	LSP16160_Scan2-015-Full-ROI	LSP16160_Scan2-014-Full-ROI	LSP16160_Scan2-013-Full-ROI	LSP16160_Scan2-012-Full-ROI	LSP16160_Scan2-011-Full-ROI	LSP16160_Scan2-010-Full-ROI	LSP16160_Scan2-009-Full-ROI	LSP16160_Scan2-008-PanCK-	LSP16160_Scan2-008-PanCK+	LSP16160_Scan2-007-PanCK-	LSP16160_Scan2-007-PanCK+	LSP16160_Scan2-006-Full-ROI	LSP16160_Scan2-005-Full-ROI	LSP16160_Scan2-004-Full-ROI	LSP16160_Scan2-003-Full-ROI	LSP16160_Scan2-002-Full-ROI	LSP16160_Scan2-001-Full-ROI	LSP16157_Scan1-035-Full-ROI	LSP16157_Scan1-034-Full-ROI	LSP16157_Scan1-033-Full-ROI	LSP16157_Scan1-032-Full-ROI	LSP16157_Scan1-031-Full-ROI	LSP16157_Scan1-030-Full-ROI	LSP16157_Scan1-029-Full-ROI	LSP16157_Scan1-028-Full-ROI	LSP16157_Scan1-027-Full-ROI	LSP16157_Scan1-026-Full-ROI	LSP16157_Scan1-025-Full-ROI	LSP16157_Scan1-024-Full-ROI	LSP16157_Scan1-023-Full-ROI	LSP16157_Scan1-022-Full-ROI	LSP16157_Scan1-021-Full-ROI	LSP16157_Scan1-020-Full-ROI	LSP16157_Scan1-019-Full-ROI	LSP16157_Scan1-018-Full-ROI	LSP16157_Scan1-017-Full-ROI	LSP16157_Scan1-016-Full-ROI	LSP16157_Scan1-015-Full-ROI	LSP16157_Scan1-014-Full-ROI	LSP16157_Scan1-013-Full-ROI	LSP16157_Scan1-011-Full-ROI	LSP16157_Scan1-010-Full-ROI	LSP16157_Scan1-009-Full-ROI	LSP16157_Scan1-008-Full-ROI	LSP16157_Scan1-007-Full-ROI	LSP16157_Scan1-006-Full-ROI	LSP16157_Scan1-005-Full-ROI	LSP16157_Scan1-004-Full-ROI	LSP16157_Scan1-003-Full-ROI	LSP16157_Scan1-002-Full-ROI	LSP16157_Scan1-001-Full-ROI	LSP16154_Scan2-013-Full-ROI	LSP16154_Scan2-012-Full-ROI	LSP16154_Scan2-011-Full-ROI	LSP16154_Scan2-010-Full-ROI	LSP16154_Scan2-009-Full-ROI	LSP16154_Scan2-008-Full-ROI	LSP16154_Scan2-007-Full-ROI	LSP16154_Scan2-006-Full-ROI	LSP16154_Scan2-005-Full-ROI	LSP16154_Scan2-004-Full-ROI	LSP16154_Scan2-003-Full-ROI	LSP16154_Scan2-002-PanCK-	LSP16154_Scan2-002-PanCK+	LSP16154_Scan2-001-PanCK-	LSP16154_Scan2-001-PanCK+	LSP16151_Scan1-008-Full-ROI	LSP16151_Scan1-007-Full-ROI	LSP16151_Scan1-006-Full-ROI	LSP16151_Scan1-005-Full-ROI	LSP16151_Scan1-004-Full-ROI	LSP16151_Scan1-003-Full-ROI	LSP16151_Scan1-002-Full-ROI	LSP16151_Scan1-001-Full-ROI	LSP16148_Scan1-009-Full-ROI	LSP16148_Scan1-008-Full-ROI	LSP16148_Scan1-007-Full-ROI	LSP16148_Scan1-006-Full-ROI	LSP16148_Scan1-005-Full-ROI	LSP16148_Scan1-004-Full-ROI	LSP16148_Scan1-003-Full-ROI	LSP16148_Scan1-002-Full-ROI	LSP16148_Scan1-001-Full-ROI	LSP16145_Scan1-026-Full-ROI	LSP16145_Scan1-025-Full-ROI	LSP16145_Scan1-024-Full-ROI	LSP16145_Scan1-023-Full-ROI	LSP16145_Scan1-022-Full-ROI	LSP16145_Scan1-021-Full-ROI	LSP16145_Scan1-020-Full-ROI	LSP16145_Scan1-015-Full-ROI	LSP16145_Scan1-014-Full-ROI	LSP16145_Scan1-013-Full-ROI	LSP16145_Scan1-011-Full-ROI	LSP16145_Scan1-006-Full-ROI	LSP16145_Scan1-005-Full-ROI	LSP16145_Scan1-004-Full-ROI	LSP16145_Scan1-003-Full-ROI	LSP16145_Scan1-002-Full-ROI	LSP16145_Scan1-001-Full-ROI	LSP16142_Scan2-018-Full-ROI	LSP16142_Scan2-016-Full-ROI	LSP16142_Scan2-015-Full-ROI	LSP16142_Scan2-014-Full-ROI	LSP16142_Scan2-013-Full-ROI	LSP16142_Scan2-012-Full-ROI	LSP16142_Scan2-011-Full-ROI	LSP16142_Scan2-010-Full-ROI	LSP16142_Scan2-009-Full-ROI	LSP16142_Scan2-008-Full-ROI	LSP16142_Scan2-007-Full-ROI	LSP16142_Scan2-006-Full-ROI	LSP16142_Scan2-005-Full-ROI	LSP16142_Scan2-004-Full-ROI	LSP16142_Scan2-003-Full-ROI	LSP16142_Scan2-002-Full-ROI	LSP16142_Scan2-001-Full-ROI	LSP16139_Scan2-027-Full-ROI	LSP16139_Scan2-026-Full-ROI	LSP16139_Scan2-025-Full-ROI	LSP16139_Scan2-024-Full-ROI	LSP16139_Scan2-023-Full-ROI	LSP16139_Scan2-022-Full-ROI	LSP16139_Scan2-021-Full-ROI	LSP16139_Scan2-020-Full-ROI	LSP16139_Scan2-019-Full-ROI	LSP16139_Scan2-018-Full-ROI	LSP16139_Scan2-017-Full-ROI	LSP16139_Scan2-016-Full-ROI	LSP16139_Scan2-015-Full-ROI	LSP16139_Scan2-014-Full-ROI	LSP16139_Scan2-013-Full-ROI	LSP16139_Scan2-012-Full-ROI	LSP16139_Scan2-011-Full-ROI	LSP16139_Scan2-010-Full-ROI	LSP16139_Scan2-009-Full-ROI	LSP16139_Scan2-008-Full-ROI	LSP16139_Scan2-007-Full-ROI	LSP16139_Scan2-006-Full-ROI	LSP16139_Scan2-005-Full-ROI	LSP16139_Scan2-004-Full-ROI	LSP16139_Scan2-003-Full-ROI	LSP16139_Scan2-002-Full-ROI	LSP16139_Scan2-001-Full-ROI	LSP15360_Scan1-022-Full-ROI	LSP15360_Scan1-021-Full-ROI	LSP15360_Scan1-020-Full-ROI	LSP15360_Scan1-019-Full-ROI	LSP15360_Scan1-018-Full-ROI	LSP15360_Scan1-017-Full-ROI	LSP15360_Scan1-016-Full-ROI	LSP15360_Scan1-015-Full-ROI	LSP15360_Scan1-014-Full-ROI	LSP15360_Scan1-013-Full-ROI	LSP15360_Scan1-012-Full-ROI	LSP15360_Scan1-011-Full-ROI	LSP15360_Scan1-010-Full-ROI	LSP15360_Scan1-009-Full-ROI	LSP15360_Scan1-008-Full-ROI	LSP15360_Scan1-007-Full-ROI	LSP15360_Scan1-006-Full-ROI	LSP15360_Scan1-005-Full-ROI	LSP15360_Scan1-004-Full-ROI	LSP15360_Scan1-003-Full-ROI	LSP15360_Scan1-002-Full-ROI	LSP15360_Scan1-001-Full-ROI	LSP15348_Scan1-011-PanCK-	LSP15348_Scan1-011-PanCK+	LSP15348_Scan1-010-Full-ROI	LSP15348_Scan1-009-PanCK-	LSP15348_Scan1-009-PanCK+	LSP15348_Scan1-008-Full-ROI	LSP15348_Scan1-007-PanCK-	LSP15348_Scan1-007-PanCK+	LSP15348_Scan1-006-PanCK-	LSP15348_Scan1-006-PanCK+	LSP15348_Scan1-005-PanCK-	LSP15348_Scan1-005-PanCK+	LSP15348_Scan1-004-PanCK-	LSP15348_Scan1-004-PanCK+	LSP15348_Scan1-003-PanCK-	LSP15348_Scan1-003-PanCK+	LSP15348_Scan1-002-PanCK-	LSP15348_Scan1-002-PanCK+	LSP15348_Scan1-001-PanCK-	LSP15348_Scan1-001-PanCK+	LSP15332_Scan1-022-PanCK+	LSP15332_Scan1-021-PanCK+	LSP15332_Scan1-020-Full-ROI	LSP15332_Scan1-019-Full-ROI	LSP15332_Scan1-018-PanCK+	LSP15332_Scan1-017-PanCK+	LSP15332_Scan1-016-PanCK+	LSP15332_Scan1-015-PanCK+	LSP15332_Scan1-014-PanCK+	LSP15332_Scan1-013-PanCK+	LSP15332_Scan1-012-PanCK-	LSP15332_Scan1-012-PanCK+	LSP15332_Scan1-011-PanCK-	LSP15332_Scan1-011-PanCK+	LSP15332_Scan1-010-PanCK-	LSP15332_Scan1-010-PanCK+	LSP15332_Scan1-009-PanCK-	LSP15332_Scan1-009-PanCK+	LSP15332_Scan1-008-PanCK-	LSP15332_Scan1-008-PanCK+	LSP15332_Scan1-007-PanCK-	LSP15332_Scan1-007-PanCK+	LSP15332_Scan1-006-PanCK-	LSP15332_Scan1-006-PanCK+	LSP15332_Scan1-005-PanCK-	LSP15332_Scan1-005-PanCK+	LSP15332_Scan1-004-PanCK-	LSP15332_Scan1-004-PanCK+	LSP15332_Scan1-003-PanCK-	LSP15332_Scan1-003-PanCK+	LSP15332_Scan1-002-PanCK-	LSP15332_Scan1-002-PanCK+	LSP15332_Scan1-001-PanCK-	LSP15332_Scan1-001-PanCK+	LSP15336_Scan1-016-PanCK+	LSP15336_Scan1-015-PanCK+	LSP15336_Scan1-014-PanCK+	LSP15336_Scan1-013-PanCK+	LSP15336_Scan1-012-PanCK+	LSP15336_Scan1-011-PanCK+	LSP15336_Scan1-010-PanCK+	LSP15336_Scan1-009-PanCK+	LSP15336_Scan1-008-PanCK+	LSP15336_Scan1-007-PanCK+	LSP15336_Scan1-006-PanCK+	LSP15336_Scan1-005-PanCK+	LSP15336_Scan1-004-PanCK+	LSP15336_Scan1-003-PanCK+	LSP15336_Scan1-002-PanCK+	LSP15336_Scan1-001-PanCK+	LSP15344_Scan1-016-PanCK+	LSP15344_Scan1-015-PanCK+	LSP15344_Scan1-014-PanCK+	LSP15344_Scan1-013-PanCK+	LSP15344_Scan1-012-PanCK+	LSP15344_Scan1-011-PanCK+	LSP15344_Scan1-010-PanCK+	LSP15344_Scan1-009-PanCK+	LSP15344_Scan1-008-PanCK+	LSP15344_Scan1-007-Full-ROI	LSP15344_Scan1-006-Full-ROI	LSP15344_Scan1-005-Full-ROI	LSP15344_Scan1-004-Full-ROI	LSP15344_Scan1-003-Full-ROI	LSP15344_Scan1-002-Full-ROI	LSP15344_Scan1-001-Full-ROI	LSP15356_Scan1-011-PanCK+	LSP15356_Scan1-010-Full-ROI	LSP15356_Scan1-009-Full-ROI	LSP15356_Scan1-008-Full-ROI	LSP15356_Scan1-007-Full-ROI	LSP15356_Scan1-006-Full-ROI	LSP15356_Scan1-005-PanCK+	LSP15356_Scan1-004-Full-ROI	LSP15356_Scan1-003-PanCK+	LSP15356_Scan1-002-PanCK+	LSP15356_Scan1-001-PanCK+	LSP15328_Scan1-012-PanCK+	LSP15328_Scan1-011-PanCK+	LSP15328_Scan1-010-PanCK+	LSP15328_Scan1-009-PanCK+	LSP15328_Scan1-008-PanCK+	LSP15328_Scan1-007-PanCK+	LSP15328_Scan1-006-PanCK+	LSP15328_Scan1-005-PanCK+	LSP15328_Scan1-004-PanCK+	LSP15328_Scan1-003-PanCK+	LSP15328_Scan1-002-PanCK+	LSP15328_Scan1-001-PanCK+	LSP15340_Scan1-022-Full-ROI	LSP15340_Scan1-021-Full-ROI	LSP15340_Scan1-017-PanCK+	LSP15340_Scan1-016-PanCK+	LSP15340_Scan1-015-PanCK+	LSP15340_Scan1-014-PanCK+	LSP15340_Scan1-013-PanCK+	LSP15340_Scan1-012-Full-ROI	LSP15340_Scan1-011-Full-ROI	LSP15340_Scan1-010-PanCK-	LSP15340_Scan1-010-PanCK+	LSP15340_Scan1-009-Full-ROI	LSP15340_Scan1-008-Full-ROI	LSP15340_Scan1-007-Full-ROI	LSP15340_Scan1-006-PanCK+	LSP15340_Scan1-005-PanCK+	LSP15340_Scan1-004-Full-ROI	LSP15340_Scan1-003-PanCK-	LSP15340_Scan1-003-PanCK+	LSP15340_Scan1-002-PanCK-	LSP15340_Scan1-002-PanCK+	LSP15340_Scan1-001-PanCK-	LSP15340_Scan1-001-PanCK+	LSP15360_Scan1-029-Full-ROI	LSP15360_Scan1-028-Full-ROI	LSP15360_Scan1-027-Full-ROI	LSP15360_Scan1-026-Full-ROI	LSP15360_Scan1-025-Full-ROI	LSP15360_Scan1-024-Full-ROI	LSP17723_Scan1-021-Full-ROI	LSP17723_Scan1-020-Full-ROI	LSP17723_Scan1-019-Full-ROI	LSP17723_Scan1-018-Full-ROI	LSP17723_Scan1-017-Full-ROI	LSP17723_Scan1-016-Full-ROI	LSP17723_Scan1-008-Full-ROI	LSP17723_Scan1-007-Full-ROI	LSP17723_Scan1-006-Full-ROI	LSP17723_Scan1-005-Full-ROI	LSP17723_Scan1-004-Full-ROI	LSP17723_Scan1-003-Full-ROI	LSP17723_Scan1-002-Full-ROI	LSP17723_Scan1-001-Full-ROI	LSP18302_scan1-020-Full-ROI	LSP18302_scan1-018-Full-ROI	LSP18302_scan1-017-Full-ROI	LSP18302_scan1-016-Full-ROI	LSP18302_scan1-015-Full-ROI	LSP18302_scan1-014-Full-ROI	LSP18302_scan1-013-Full-ROI	LSP18302_scan1-012-Full-ROI	LSP18302_scan1-011-Full-ROI	LSP18302_scan1-010-Full-ROI	LSP18302_scan1-009-Full-ROI	LSP18302_scan1-008-Full-ROI	LSP18302_scan1-007-Full-ROI	LSP18302_scan1-006-Full-ROI	LSP18302_scan1-005-Full-ROI	LSP18302_scan1-004-Full-ROI	LSP18302_scan1-003-Full-ROI	LSP18302_scan1-002-Full-ROI	LSP18302_scan1-001-Full-ROI	LSP18306_scan1-009-Full-ROI	LSP18306_scan1-008-Full-ROI	LSP18306_scan1-007-Full-ROI	LSP18306_scan1-006-Full-ROI	LSP18306_scan1-005-Full-ROI	LSP18306_scan1-004-Full-ROI	LSP18306_scan1-003-Full-ROI	LSP18306_scan1-002-Full-ROI	LSP18306_scan1-001-Full-ROI	LSP17803_Scan1-007-Full-ROI	LSP17803_Scan1-006-Full-ROI	LSP17803_Scan1-005-Full-ROI	LSP17803_Scan1-004-Full-ROI	LSP17803_Scan1-003-Full-ROI	LSP17803_Scan1-002-Full-ROI	LSP17803_Scan1-001-Full-ROI	LSP18318_scan1-021-Full-ROI	LSP18318_scan1-020-Full-ROI	LSP18318_scan1-019-Full-ROI	LSP18318_scan1-018-Full-ROI	LSP18318_scan1-017-Full-ROI	LSP18318_scan1-016-Full-ROI	LSP18318_scan1-015-Full-ROI	LSP18318_scan1-014-Full-ROI	LSP18318_scan1-013-Full-ROI	LSP18318_scan1-012-Full-ROI	LSP18318_scan1-011-Full-ROI	LSP18318_scan1-010-Full-ROI	LSP18318_scan1-009-Full-ROI	LSP18318_scan1-008-Full-ROI	LSP18318_scan1-007-Full-ROI	LSP18318_scan1-006-Full-ROI	LSP18318_scan1-005-Full-ROI	LSP18318_scan1-004-Full-ROI	LSP18318_scan1-003-Full-ROI	LSP18318_scan1-002-Full-ROI	LSP18318_scan1-001-Full-ROI	LSP17851_Scan1-012-Full-ROI	LSP17851_Scan1-011-Full-ROI	LSP17851_Scan1-010-Full-ROI	LSP17851_Scan1-009-Full-ROI	LSP17851_Scan1-008-Full-ROI	LSP17851_Scan1-006-Full-ROI	LSP17851_Scan1-004-Full-ROI	LSP17851_Scan1-003-Full-ROI	LSP17851_Scan1-002-Full-ROI	LSP17851_Scan1-001-Full-ROI	LSP17819_Scan1-007-Full-ROI	LSP17819_Scan1-006-Full-ROI	LSP17819_Scan1-005-Full-ROI	LSP17819_Scan1-004-Full-ROI	LSP17819_Scan1-003-Full-ROI	LSP17819_Scan1-002-Full-ROI	LSP17819_Scan1-001-Full-ROI	LSP18314_scan1-026-Full-ROI	LSP18314_scan1-023-Full-ROI	LSP18314_scan1-015-Full-ROI	LSP18314_scan1-004-Full-ROI	LSP18314_scan1-003-Full-ROI	LSP17727_Scan1-014-Full-ROI	LSP17727_Scan1-013-Full-ROI	LSP17727_Scan1-010-Full-ROI	LSP17727_Scan1-009-Full-ROI	LSP17727_Scan1-008-Full-ROI	LSP17727_Scan1-007-Full-ROI	LSP17727_Scan1-004-Full-ROI	LSP17727_Scan1-002-Full-ROI	LSP17727_Scan1-001-Full-ROI	LSP18310_scan1-019-Full-ROI	LSP18310_scan1-018-Full-ROI	LSP18310_scan1-017-Full-ROI	LSP18310_scan1-016-Full-ROI	LSP18310_scan1-015-Full-ROI	LSP18310_scan1-014-Full-ROI	LSP18310_scan1-013-Full-ROI	LSP18310_scan1-012-Full-ROI	LSP18310_scan1-011-Full-ROI	LSP18310_scan1-010-Full-ROI	LSP18310_scan1-009-Full-ROI	LSP18310_scan1-008-Full-ROI	LSP18310_scan1-007-Full-ROI	LSP18310_scan1-006-Full-ROI	LSP18310_scan1-005-Full-ROI	LSP18310_scan1-004-Full-ROI	LSP18310_scan1-003-Full-ROI	LSP18310_scan1-002-Full-ROI	LSP18310_scan1-001-Full-ROI	LSP17731_Scan1-019-Full-ROI	LSP17731_Scan1-018-Full-ROI	LSP17731_Scan1-017-Full-ROI	LSP17731_Scan1-016-Full-ROI	LSP17731_Scan1-015-Full-ROI	LSP17731_Scan1-012-Full-ROI	LSP17731_Scan1-011-Full-ROI	LSP17731_Scan1-010-Full-ROI	LSP17731_Scan1-009-Full-ROI	LSP17731_Scan1-008-Full-ROI	LSP17731_Scan1-007-Full-ROI	LSP17731_Scan1-006-Full-ROI	LSP17731_Scan1-005-Full-ROI	LSP17731_Scan1-004-Full-ROI	LSP17731_Scan1-003-Full-ROI	LSP17731_Scan1-002-Full-ROI	LSP17731_Scan1-001-Full-ROI	LSP17763_Scan1-008-Full-ROI	LSP17763_Scan1-007-Full-ROI	LSP17763_Scan1-006-Full-ROI	LSP17763_Scan1-005-Full-ROI	LSP17763_Scan1-004-Full-ROI	LSP17763_Scan1-003-Full-ROI	LSP17763_Scan1-002-Full-ROI	LSP17763_Scan1-001-Full-ROI	LSP17823_Scan1-012-Full-ROI	LSP17823_Scan1-011-Full-ROI	LSP17823_Scan1-010-Full-ROI	LSP17823_Scan1-009-Full-ROI	LSP17823_Scan1-008-Full-ROI	LSP17823_Scan1-007-Full-ROI	LSP17823_Scan1-006-Full-ROI	LSP17823_Scan1-005-Full-ROI	LSP17823_Scan1-004-Full-ROI	LSP17823_Scan1-003-Full-ROI	LSP17823_Scan1-002-Full-ROI	LSP17823_Scan1-001-Full-ROI	LSP17723_Scan1-015-Full-ROI	LSP17723_Scan1-014-Full-ROI	LSP17723_Scan1-013-Full-ROI	LSP17723_Scan1-012-Full-ROI	LSP17723_Scan1-011-Full-ROI	LSP17723_Scan1-010-Full-ROI	LSP17723_Scan1-009-Full-ROI	LSP17823_Scan1-013-Full-ROI	LSP19411_Scan1-025-Full-ROI	LSP19411_Scan1-024-Full-ROI	LSP19411_Scan1-023-Full-ROI	LSP19411_Scan1-022-Full-ROI	LSP19411_Scan1-021-Full-ROI	LSP19411_Scan1-020-Full-ROI	LSP19411_Scan1-019-Full-ROI	LSP19411_Scan1-018-Full-ROI	LSP19411_Scan1-017-Full-ROI	LSP19411_Scan1-016-Full-ROI	LSP19411_Scan1-015-Full-ROI	LSP19411_Scan1-014-Full-ROI	LSP19411_Scan1-013-Full-ROI	LSP19411_Scan1-012-Full-ROI	LSP19411_Scan1-011-Full-ROI	LSP19411_Scan1-010-Full-ROI	LSP19411_Scan1-009-Full-ROI	LSP19411_Scan1-008-Full-ROI	LSP19411_Scan1-007-Full-ROI	LSP19411_Scan1-006-Full-ROI	LSP19411_Scan1-005-Full-ROI	LSP19411_Scan1-003-Full-ROI	LSP19421_Scan1-019-Full-ROI	LSP19421_Scan1-016-Full-ROI	LSP19421_Scan1-015-Full-ROI	LSP19421_Scan1-014-Full-ROI	LSP19421_Scan1-013-Full-ROI	LSP19421_Scan1-012-Full-ROI	LSP19421_Scan1-011-Full-ROI	LSP19421_Scan1-010-Full-ROI	LSP19421_Scan1-009-Full-ROI	LSP19421_Scan1-008-Full-ROI	LSP19421_Scan1-007-Full-ROI	LSP19421_Scan1-006-Full-ROI	LSP19421_Scan1-005-Full-ROI	LSP19421_Scan1-004-Full-ROI	LSP19421_Scan1-003-Full-ROI	LSP19421_Scan1-002-Full-ROI	LSP19421_Scan1-001-Full-ROI	LSP19417_Scan1-013-Full-ROI	LSP19417_Scan1-012-Full-ROI	LSP19417_Scan1-011-Full-ROI	LSP19417_Scan1-010-Full-ROI	LSP19417_Scan1-009-Full-ROI	LSP19417_Scan1-008-Full-ROI	LSP19417_Scan1-007-Full-ROI	LSP19417_Scan1-006-Full-ROI	LSP19417_Scan1-005-Full-ROI	LSP19417_Scan1-004-Full-ROI	LSP19417_Scan1-003-Full-ROI	LSP19417_Scan1-002-Full-ROI	LSP19417_Scan1-001-Full-ROI	LSP19407_Scan1-010-Full-ROI	LSP19407_Scan1-009-Full-ROI	LSP19407_Scan1-008-Full-ROI	LSP19407_Scan1-007-Full-ROI	LSP19407_Scan1-006-Full-ROI	LSP19407_Scan1-005-Full-ROI	LSP19407_Scan1-004-Full-ROI	LSP19407_Scan1-003-Full-ROI	LSP19407_Scan1-002-Full-ROI	LSP19407_Scan1-001-Full-ROI	LSP19409_Scan1-013-Full-ROI	LSP19409_Scan1-012-Full-ROI	LSP19409_Scan1-011-Full-ROI	LSP19409_Scan1-010-Full-ROI	LSP19409_Scan1-009-Full-ROI	LSP19409_Scan1-008-Full-ROI	LSP19409_Scan1-007-Full-ROI	LSP19409_Scan1-005-Full-ROI	LSP19409_Scan1-004-Full-ROI	LSP19409_Scan1-003-Full-ROI	LSP19409_Scan1-002-Full-ROI	LSP19409_Scan1-001-Full-ROI	LSP19413_Scan1-014-Full-ROI	LSP19413_Scan1-013-Full-ROI	LSP19413_Scan1-012-Full-ROI	LSP19413_Scan1-011-Full-ROI	LSP19413_Scan1-010-Full-ROI	LSP19413_Scan1-009-Full-ROI	LSP19413_Scan1-008-Full-ROI	LSP19413_Scan1-007-Full-ROI	LSP19413_Scan1-006-Full-ROI	LSP19413_Scan1-005-Full-ROI	LSP19413_Scan1-004-Full-ROI	LSP19413_Scan1-003-Full-ROI	LSP19413_Scan1-002-Full-ROI	LSP19413_Scan1-001-Full-ROI	LSP19421_Scan1-017-Full-ROI

public/ovary_geomx_gray_foundation_2024/meta_cell_intensity.txt

@@ -0,0 +1,12 @@
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+genetic_alteration_type: GENERIC_ASSAY
+generic_assay_type: RFU_P53_MARKER_INTENSITY
+datatype: LIMIT-VALUE
+stable_id: rfu_p53_marker_intensity
+profile_name: p53 Marker Intensity
+profile_description: p53 Marker Intensity
+data_filename: data_cell_intensity.txt
+show_profile_in_analysis_tab: true
+pivot_threshold_value: 0.001
+value_sort_order: ASC
+generic_entity_meta_properties: NAME

public/ovary_geomx_gray_foundation_2024/meta_cell_type_fractions.txt

@@ -0,0 +1,12 @@
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+genetic_alteration_type: GENERIC_ASSAY
+generic_assay_type: CYCIF_CELL_TYPE_FRACTIONS
+datatype: LIMIT-VALUE
+stable_id: cycif_cell_type_fractions
+profile_name: CyCIF - Cell Type Fractions
+profile_description: Cell type fractions
+data_filename: data_cell_type_fractions.txt
+show_profile_in_analysis_tab: true
+pivot_threshold_value: 0.001
+value_sort_order: ASC
+generic_entity_meta_properties: NAME

public/ovary_geomx_gray_foundation_2024/meta_clinical_patient.txt

@@ -0,0 +1,4 @@
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt

public/ovary_geomx_gray_foundation_2024/meta_clinical_sample.txt

@@ -0,0 +1,4 @@
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt

public/ovary_geomx_gray_foundation_2024/meta_mrna_seq_expression.txt

@@ -0,0 +1,8 @@
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: CONTINUOUS
+data_filename: data_mrna_seq_expression.txt
+stable_id: rna_seq_mrna
+show_profile_in_analysis_tab: true
+profile_description: RNA seq expression levels obtained from GeOmx (Z-scores compared to all samples normalized and transformed)
+profile_name: mRNA-Seq Expression GeoMx

public/ovary_geomx_gray_foundation_2024/meta_resource_definition.txt

@@ -0,0 +1,3 @@
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+resource_type: DEFINITION
+data_filename: data_resource_definition.txt

public/ovary_geomx_gray_foundation_2024/meta_resource_sample.txt

@@ -0,0 +1,3 @@
+cancer_study_identifier: ovary_geomx_gray_foundation_2024
+resource_type: SAMPLE
+data_filename: data_resource_sample.txt