Archive 4 checkpoints (1-4)

paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/FINDINGS.json

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+{
+ "sc_chemistry": {
+  "geo_statement": "GEX GSMs: '10xGenomics Single Cell 3' Library Gel Bead Kit V3.1'; VDJ GSMs: '10xGenomics Single Cell 5' RNA, VDJ Library Gel Bead Kit'",
+  "first_barcode_prefix_counts": {
+   "AAACCTG": 133
+  },
+  "barcode_suffixes": [
+   "1"
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+  "tcr_contig_cells_found_among_gex_barcodes": {
+   "median": 0.994665085951393,
+   "min": 0.5223458038422649,
+   "pooled": 0.9816102123356926
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+  "conclusion": "GEX barcodes come from the 737K-august-2016 whitelist (every library's sorted first barcode starts AAACCTG; 3' v3/v3.1 uses the 3M-february-2018 list) and nearly all TCR contig cells are GEX cells. The GEX was therefore captured in the same 5' GEM reaction as the V(D)J libraries: 10x 5' gene expression, not 3' v3.1 as the GEO GEX records state.",
+  "mtx_header": "cellranger-6.1.1 (MatrixMarket metadata_json)",
+  "features_file_identical_across_libraries": true
+ },
+ "author_filtering": {
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+  "cells_at_or_above_20pct_mito": 20487,
+  "cells_at_or_above_2x_median_genes": 39338,
+  "conclusion": "GEO matrices are Cell Ranger cell-called barcodes (no cell under 500 UMIs) but NOT the authors' Seurat-filtered set: cells violating the stated MT%<20, genes>200 and genes<2x median rules remain."
+ },
+ "sex_vs_geo": {
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+    "sc_sample_id": "Uri-S112",
+    "sc_gender": "Male",
+    "sc_sex_call": "female"
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+    "bulk_Ysum_cpm": 1.5057275617858994
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+  ]
+ }
+}

paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/SOURCES.json

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paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/extracted/GSE279448.extraction_receipt.json

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