diff --git a/paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/pairing/PAIRING_SUMMARY.json b/paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/pairing/PAIRING_SUMMARY.json new file mode 100644 index 0000000000000000000000000000000000000000..f3937fd320d996d5b8302fc6be7ebaacfbdc723d --- /dev/null +++ b/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 ' joined to bulk title 'bulkRNA ': 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." +} diff --git a/paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/singlecell/SINGLECELL_SUMMARY.json b/paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/singlecell/SINGLECELL_SUMMARY.json new file mode 100644 index 0000000000000000000000000000000000000000..5ead5e4dfadf0ff877e12f04c81d03ef0f9f0b04 --- /dev/null +++ b/paper-releases/20260928/diffusion/data/source_provenance/ye2026_sepsis/singlecell/SINGLECELL_SUMMARY.json @@ -0,0 +1,14103 @@ +{ + "created_at_utc": "2026-09-27T06:04:18.665948+00:00", + "libraries": [ + { + "accession": "GSE279452", + "library_id": "GSM8571082", + "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ye2026_sepsis_v1_20260927/extracted/GSE279452/GSM8571082_Abd-PS04.matrix.mtx.gz", + "format": "mtx", + "duplicate_representation": false, + "features_path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ye2026_sepsis_v1_20260927/extracted/GSE279452/GSM8571082_Abd-PS04.features.tsv.gz", + "barcodes_path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ye2026_sepsis_v1_20260927/extracted/GSE279452/GSM8571082_Abd-PS04.barcodes.tsv.gz", + "sample_id_sc_title": "Abd-PS04", + "status": "PASS", + "output_dir": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ye2026_sepsis_v1_20260927/singlecell/GSM8571082", + "started": "2026-09-27T05:58:09.438632+00:00", + "n_cells": 5668, + "n_features": 37487, + "n_rna_features": 37487, + "n_qc_review_pass": 5449, + "flag_counts": { + "zero_total": 0, + "low_genes_200": 70, + "low_abundance_500": 0, + "mito_above_20pct": 155, + "low_total_mad": 0, + "low_genes_mad": 11, + "high_mito_mad": 346, + "high_total_review_only": 0, + "structural_nonempty": 5668, + "conservative_review_pass": 5449 + }, + "numeric": { + "minimum_stored": 1.0, + "maximum_stored": 18474.0, + "integer_fraction_stored": 1.0, + "integer_fraction_selected_stored": 1.0, + "raw_counts_proven": false, + "interpretation": "Integer-valued entries do not establish raw-count provenance; 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