Archive 4 checkpoints (1-4)

paper-releases/20260928/diffusion/data/source_provenance/imperial_eskd/singlecell/gene_mapping.summary.json

@@ -0,0 +1,32 @@
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+  "presence_mask_semantics": "source_feature_table_membership;not_detection_or_proof_of_assay_coverage",
+  "absent_feature_policy": "masked_missing;never_observed_zero",
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+}

paper-releases/20260928/diffusion/data/source_provenance/ji2025_chili/SOURCES.json

@@ -0,0 +1,62 @@
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+}

paper-releases/20260928/diffusion/data/source_provenance/ji2025_chili/pairing/PAIRING_SUMMARY.json

@@ -0,0 +1,92 @@
+{
+  "bulk_gsms": 128,
+  "bulk_subjects": 61,
+  "sc_gsms_total": 92,
+  "sc_gex_gsms": 46,
+  "sc_tcr_gsms": 46,
+  "sc_gex_patients": 28,
+  "sc_gex_patient_visits": 45,
+  "tcr_library_keys_equal_gex": true,
+  "pairs_total": 40,
+  "pairs_patients": 23,
+  "pairs_by_timepoint": {
+    "AC": 13,
+    "TOL": 10,
+    "BC": 9,
+    "FU1": 8
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+  "pairs_by_outcome": {
+    "control": 22,
+    "ChILI": 18
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+  "pairs_by_id_match": {
+    "exact_subject_id": 39,
+    "zero_padding_difference": 1
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+  "pairs_per_patient": {
+    "1": 6,
+    "2": 17
+  },
+  "pairs_with_metadata_notes": [
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+      "sample_id": "N043_TOL",
+      "metadata_notes": "steroid bulk n vs sc y"
+    },
+    {
+      "sample_id": "N128_AC",
+      "metadata_notes": "age bulk 61 vs sc 62"
+    },
+    {
+      "sample_id": "N129_AC",
+      "metadata_notes": "age bulk 50 vs sc 51"
+    }
+  ],
+  "bulk_matched_by_multiple_sc": {},
+  "sc_without_bulk": [
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+      "sc_gsm": "GSM8747412",
+      "sample_id": "N014_BC",
+      "unpaired_reason": "no bulk for N014 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
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+    {
+      "library_key": "Rd1_N016V01",
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+      "sample_id": "N016_BC",
+      "unpaired_reason": "no bulk for N016 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
+    },
+    {
+      "library_key": "Rd1_N037V01",
+      "sc_gsm": "GSM8747422",
+      "sample_id": "N037_BC",
+      "unpaired_reason": "no bulk for N037 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
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+    {
+      "library_key": "Rd4a_N131V01",
+      "sc_gsm": "GSM8747460",
+      "sample_id": "N131_TOL",
+      "unpaired_reason": "no bulk for N131 at TOL; bulk timepoints of this patient: BC"
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+    {
+      "library_key": "Rd4a_N127V00",
+      "sc_gsm": "GSM8747462",
+      "sample_id": "N127_BC",
+      "unpaired_reason": "no bulk for N127 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
+    },
+    {
+      "library_key": "Rd5_N131V01",
+      "sc_gsm": "GSM8747488",
+      "sample_id": "N131_TOL",
+      "unpaired_reason": "no bulk for N131 at TOL; bulk timepoints of this patient: BC"
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+  "bulk_without_sc": 88,
+  "bulk_without_sc_by_timepoint": {
+    "BC": 39,
+    "AC": 24,
+    "TOL": 12,
+    "FU2": 7,
+    "FU1": 6
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+  "rule": "Pair = same patient AND same GEO timepoint label. Patient = GEO 'subject' (bulk: 'N064'; sc: the N### prefix of PID_visit 'N064V01'), zero-padded to 3 digits (bulk writes N87/N96 for N087/N096). Timepoint = GEO 'time' (BC/AC/TOL/FU1/FU2; for sc also equal to the Seurat per-cell Time). An accepted pair must also agree on GEO sex, outcome group (chili/control) and ICI regimen, and age within 1 year (differences recorded); steroid-status differences are recorded, not refused. A bulk sample may pair with only one sc library. TCR GSMs are separate V(D)J libraries and are not paired."
+}