Archive 2 checkpoints (1-2)

paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/pairing/PAIRING_SUMMARY.json

@@ -0,0 +1,86 @@
+{
+  "bulk_gsms": 207,
+  "sc_gsms_total": 266,
+  "sc_gex_gsms": 133,
+  "sc_vdj_gsms": 133,
+  "vdj_sample_ids_equal_gex_sample_ids": true,
+  "pairs_by_id_match": {
+    "exact_title": 80,
+    "case_only_title_difference": 4,
+    "missing_S_letter_in_sc_title": 1
+  },
+  "pairs_total": 85,
+  "pairs_by_group": {
+    "adult_sepsis": 48,
+    "ped_sepsis": 16,
+    "adult_HC": 7,
+    "adult_ICU_ctrl": 6,
+    "ped_HC": 4,
+    "ped_ICU_ctrl": 4
+  },
+  "sc_without_bulk": [
+    "Abd-PS18",
+    "Abd-S101",
+    "Abd-S11",
+    "Abd-S111",
+    "Abd-S12",
+    "Abd-S13",
+    "Abd-S23",
+    "Abd-S45",
+    "Abd-S49",
+    "Abd-S53",
+    "Abd-S55",
+    "Abd-S58",
+    "Abd-S59",
+    "Abd-S67",
+    "Abd-S72",
+    "Abd-S73",
+    "Abd-S75",
+    "Abd-S80",
+    "Abd-S81",
+    "Abd-S9",
+    "Abd-S91",
+    "CNS-S189",
+    "CNS-S50",
+    "CNS-S61",
+    "IC08",
+    "IC09",
+    "Res-S70",
+    "Res-S100",
+    "Res-S110",
+    "RES-S118",
+    "Res-S144",
+    "Res-S145",
+    "Res-S15",
+    "Res-S167",
+    "Res-S168",
+    "Res-S170",
+    "RES-S176",
+    "Res-S18",
+    "Res-S183",
+    "Res-S21",
+    "Res-S22",
+    "Res-S3",
+    "Res-S32",
+    "Res-S41",
+    "Res-S56",
+    "Uri-S116",
+    "Uri-S85",
+    "Uri-S88"
+  ],
+  "sc_without_bulk_by_group": {
+    "adult_sepsis": 45,
+    "adult_ICU_ctrl": 2,
+    "ped_sepsis": 1
+  },
+  "bulk_without_sc": 122,
+  "bulk_without_sc_by_group": {
+    "adult_sepsis": 68,
+    "adult_HC": 36,
+    "adult_ICU_ctrl": 17,
+    "ped_ICU_ctrl": 1
+  },
+  "metadata_mismatches_among_matches": 0,
+  "timepoints": "none: every sample ID occurs once per series; GEO has no visit/time field",
+  "rule": "sc GEX GSM title 'scRNA <ID>' joined to bulk title 'bulkRNA <ID>': exact ID first, then case-insensitive, then source-prefixed IDs with the missing 'S' patient-type letter restored; every accepted match must also agree on GEO sex, age, group, infection source and collection site. VDJ GSMs are separate 5' VDJ libraries and are not paired."
+}