Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261006T054909Z-fig1-corpus-panels/diffusion/dataset/server_1/manuscript/source_data/corpus/corpus_summary.json

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+  "MDS/MPN": 130268,
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+  "SLE": 792660
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+ "family_cells": {
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+  "Drug reaction": 25272,
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+  "Healthy": 36639276,
+  "Infection": 1396029
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+ "handling_cells": {
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+  "in vitro": 9773763
+ },
+ "cmv_seropositive_healthy_cells": 9215690,
+ "assay_cells": {
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+  "10x Flex": 3758514,
+  "10x v2 (3'/5')": 34051,
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+ "platform_cells": {
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+ "celltype_l1_cells": {
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+  "No label (overlay)": 124405,
+  "Platelet": 121626,
+  "Progenitor cell": 1206741,
+  "T cell": 24772208,
+  "__unknown__": 158160
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+ "corpus_vs_block_donor_id_mismatch_rows": 0,
+ "donors_in_more_than_one_split": 7,
+ "cells_of_those_donors": 2291988,
+ "donors_in_more_than_one_split_by_dataset": {
+  "061_A_": 6,
+  "300b_A": 1
+ },
+ "conditions_order": [
+  "Healthy",
+  "SLE",
+  "RA",
+  "ACPA+ at risk of RA",
+  "JDM",
+  "COVID-19",
+  "Post-COVID-19",
+  "Influenza",
+  "MDS",
+  "MDS/MPN",
+  "Cytopenia",
+  "DRESS"
+ ],
+ "condition_family": {
+  "Healthy": "Healthy",
+  "SLE": "Autoimmune",
+  "RA": "Autoimmune",
+  "ACPA+ at risk of RA": "Autoimmune",
+  "JDM": "Autoimmune",
+  "COVID-19": "Infection",
+  "Post-COVID-19": "Infection",
+  "Influenza": "Infection",
+  "MDS": "Haematological",
+  "MDS/MPN": "Haematological",
+  "Cytopenia": "Haematological",
+  "DRESS": "Drug reaction"
+ },
+ "inputs": {
+  "corpus_obs": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source/metadata/obs_sc.parquet",
+  "block_obs": "/home/sj_server_1/PBISC/PBISC-data/single-cell-data-block-blood/metadata/obs_sc.parquet",
+  "sample_index": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_index/metadata/sample_index.parquet",
+  "source_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/data/e2_full_source/dataset_manifest.json",
+  "geo": [
+   "GSE132802_series_matrix.txt.gz",
+   "GSE163121_series_matrix.txt.gz",
+   "GSE274680_series_matrix.txt.gz",
+   "GSE314010_series_matrix.txt.gz"
+  ]
+ },
+ "script": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/scripts/corpus/build_corpus_tables.py"
+}

paper-releases/pbisc-diffusion/updates/20261006T054909Z-fig1-corpus-panels/diffusion/dataset/server_1/manuscript/source_data/corpus/dataset_info.csv

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+dataset_prefix,short_name,accession,enrichment,metadata_note
+001_A,Perez SLE,CELLxGENE 436154da,PBMC,disease from source obs
+005_A,OneK1K,CELLxGENE dde06e0f,PBMC,disease from source obs
+006_A,AIDA,CELLxGENE ced320a1,PBMC,disease from source obs
+007_A,Miao RA,CELLxGENE e1a9ca56,PBMC,disease from source obs
+009_A,Human Immune Health Atlas,AIFI HIHA,PBMC,CMV-seropositive healthy donors are recorded as cytomegalovirus infection
+010_A,ScaleBio PBMC,CELLxGENE 4a9fd4d7,PBMC,disease from source obs
+053_B,CITE-seq PBMC,CELLxGENE b0cf0afa,PBMC,disease from source obs
+058_B,COVID-19 immunodeficiency,CELLxGENE eb735cc9,PBMC,disease from source obs
+061_A,RA at-risk cohort,GSE274680,PBMC,group from GEO sample title suffix (CON1/CON2 control; ARI/LONG ACPA+ at risk; ERA early RA); subject from GEO characteristics
+065_A,Sound Life,GSE271896,PBMC,CMV-seropositive healthy donors are recorded as cytomegalovirus infection; flu-vaccine draws
+071_C,JDM CITE-seq,CELLxGENE,PBMC,disease from source obs
+074_A,COMBAT,CELLxGENE COMBAT,PBMC,disease from source obs
+081_B,SARS-CoV-2 Seq-Well,CELLxGENE,PBMC,disease from source obs
+093_C,SARS-CoV-2 local and systemic,CELLxGENE,PBMC,disease from source obs
+200_A,Immunobiology of Aging,GSE275067,PBMC,CMV-seropositive healthy donors are recorded as cytomegalovirus infection
+202_B,COVID-19 time course,GSE161918,PBMC,disease from source obs
+203_B,Indonesia diversity,CELLxGENE 665714af,PBMC,disease from source obs
+204_B,Circulating HSPC (aging/MDS),CELLxGENE,HSPC-enriched,hematologic disorder = cytopenia; MDS/MPN includes CMML (source diagnosis column)
+300b_A,DRESS,GSE132802,PBMC,one DRESS patient (fresh and cultured PBMC) and one healthy volunteer (GEO); 10x 3'/5' v2
+301_A,SLE B cells,GSE163121,B-cell enriched,2 healthy controls and 3 SLE (GEO); 10x 3' v2
+302_A,IL-36 stimulation,GSE314010,PBMC,5 healthy donors; each split into unstimulated and IL-36-stimulated (7 h) halves (GEO)
+304_A,Parse 10M cytokines,Parse Biosciences,PBMC,12 healthy donors; 90 cytokines or PBS for 24 h; 1092 conditions (https://www.parsebiosciences.com/datasets/10-million-human-pbmcs-in-a-single-experiment/)

paper-releases/pbisc-diffusion/updates/20261006T054909Z-fig1-corpus-panels/diffusion/dataset/server_1/manuscript/source_data/corpus/geo/GSE132802_series_matrix.txt.gz

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paper-releases/pbisc-diffusion/updates/20261006T054909Z-fig1-corpus-panels/diffusion/dataset/server_1/manuscript/source_data/corpus/geo/GSE163121_series_matrix.txt.gz

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