{"registry": [{"id": "GSE169159", "acc": "GSE169159", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "whole blood / PBMC", "assay": "bulk RNA-seq + scRNA-seq", "n": "185 samples (56 enrolled, ~32 bulk)", "status": "confirmed", "recipe": true, "roles": "anchor, prime_vs_boost, baseline_predictor", "notes": ""}, {"id": "GSE195673", "acc": "GSE195673", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "PBMC + lymph node + bone marrow", "assay": "scRNA-seq + 10x VDJ (BCR)", "n": "8 single-cell subjects", "status": "literature", "recipe": false, "roles": "anchor, lymph_node, single_cell", "notes": ""}, {"id": "GSE190001", "acc": "GSE190001", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2 + mRNA-1273", "platform": "mRNA", "species": "human", "tissue": "whole blood (fingerstick)", "assay": "3' bulk RNA-seq", "n": "23 volunteers, 440 profiles", "status": "literature", "recipe": true, "roles": "anchor, kinetics, prime_vs_boost, baseline_predictor", "notes": ""}, {"id": "GSE220682", "acc": "GSE220682", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "203", "status": "catalog", "recipe": true, "roles": "discovery, variability, baseline_predictor", "notes": ""}, {"id": "GSE190747", "acc": "GSE190747", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "30", "status": "catalog", "recipe": false, "roles": "validation", "notes": ""}, {"id": "GSE209985", "acc": "GSE209985", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "32", "status": "catalog", "recipe": false, "roles": "validation", "notes": ""}, {"id": "GSE246525", "acc": "GSE246525", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "10", "status": "catalog", "recipe": false, "roles": "validation", "notes": ""}, {"id": "GSE250023", "acc": "GSE250023", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "18", "status": "catalog", "recipe": false, "roles": "validation", "notes": ""}, {"id": "GSE265975", "acc": "GSE265975", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "29", "status": "catalog", "recipe": false, "roles": "validation", "notes": ""}, {"id": "GSE281864", "acc": "GSE281864", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "17", "status": "catalog", "recipe": false, "roles": "validation", "notes": ""}, {"id": "GSE246937", "acc": "GSE246937", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "whole blood", "assay": "scRNA-seq", "n": "10", "status": "catalog", "recipe": false, "roles": "single_cell", "notes": ""}, {"id": "GSE247917", "acc": "GSE247917", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "BNT162b2", "platform": "mRNA", "species": "human", "tissue": "PBMC", "assay": "scRNA-seq", "n": "14", "status": "catalog", "recipe": false, "roles": "single_cell", "notes": ""}, {"id": "GSE247901", "acc": "GSE247901", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "mRNA SARS-CoV-2 vaccine", "platform": "mRNA", "species": "human", "tissue": "peripheral blood", "assay": "multimodal scRNA-seq + BCR/TCR", "n": "not stated", "status": "literature", "recipe": false, "roles": "single_cell, prime_vs_boost, baseline_predictor", "notes": ""}, {"id": "GSE276544", "acc": "GSE276544", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "ChAdOx1 / BNT162b2 / MVA / mRNA-1273", "platform": "multi", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "43", "status": "catalog", "recipe": false, "roles": "cross_platform", "notes": ""}, {"id": "GSE247401", "acc": "GSE247401", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "ChAdOx1 / BNT162b2 / mRNA-1273", "platform": "multi", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "17", "status": "catalog", "recipe": false, "roles": "cross_platform", "notes": ""}, {"id": "GSE201533", "acc": "GSE201533", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "ChAdOx1 / BNT162b2", "platform": "multi", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "43", "status": "catalog", "recipe": true, "roles": "cross_platform, prime_vs_boost", "notes": ""}, {"id": "GSE201642", "acc": "GSE201642", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "ChAdOx1 / BNT162b2", "platform": "multi", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "15", "status": "catalog", "recipe": false, "roles": "cross_platform", "notes": ""}, {"id": "GSE199750", "acc": "GSE199750", "section": "covid_mrna", "pathogen": "SARS-CoV-2", "vaccine": "ChAdOx1 / BNT162b2", "platform": "multi", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "86", "status": "catalog", "recipe": false, "roles": "cross_platform", "notes": "RAW.tar is 824 MB of per-sample featureCounts; visit codes V0/V1/V2A/V3A need the paper to decode"}, {"id": "GSE318946", "acc": "GSE318946", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "Novavax NVX + ChAdOx1", "platform": "multi", "species": "human", "tissue": "PBMC", "assay": "scRNA-seq + bulk RNA-seq", "n": "44 PBMC samples / 22 donors", "status": "literature", "recipe": false, "roles": "cross_platform, single_cell", "notes": ""}, {"id": "GSE320554", "acc": "GSE320554", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "NVX + ChAdOx1 + BNT162b2", "platform": "multi", "species": "human", "tissue": "blood + scRNA", "assay": "transcriptomics + cytokines + Ab", "n": "161 volunteers", "status": "literature", "recipe": false, "roles": "cross_platform", "notes": ""}, {"id": "GSE201534", "acc": "GSE201534", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "ChAdOx1->BNT162b2 vs BNT162b2/BNT162b2", "platform": "heterologous", "species": "human", "tissue": "PBMC", "assay": "scRNA-seq + bulk RNA-seq", "n": "6 single-cell / 46 cohort", "status": "literature", "recipe": false, "roles": "cross_platform, single_cell", "notes": ""}, {"id": "GSE228839", "acc": "GSE228839, GSE228841", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "ChAdOx1 nCoV-19 vs MenACWY", "platform": "adenovector", "species": "human", "tissue": "blood", "assay": "bulk RNA-seq + small RNA-seq", "n": "180 samples", "status": "literature", "recipe": false, "roles": "breakthrough", "notes": ""}, {"id": "HRA004001", "acc": "HRA004001, OMIX003038, PRJCA004747", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "BBIBP-CorV", "platform": "inactivated", "species": "human", "tissue": "PBMC", "assay": "scRNA-seq + scTCR/scBCR", "n": "44 samples", "status": "literature", "recipe": false, "roles": "single_cell", "notes": ""}, {"id": "CoronaVac-scRNA", "acc": "", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "CoronaVac", "platform": "inactivated", "species": "human", "tissue": "PBMC", "assay": "scRNA-seq + scTCR/scBCR", "n": "6 donors", "status": "none", "recipe": false, "roles": "", "notes": ""}, {"id": "CRR119890", "acc": "CRR119890, CRR125445, CRR125446, CRR119891, CRR119892, CRR119893", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "CoronaVac", "platform": "inactivated", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "29 vaccinees not deposited", "status": "literature", "recipe": false, "roles": "", "notes": ""}, {"id": "GSE302672", "acc": "GSE302672", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "Ad5 vs mRNA vs protein (mouse)", "platform": "multi", "species": "mouse", "tissue": "draining LN + PBMC", "assay": "scRNA-seq", "n": "5 mice/group", "status": "literature", "recipe": false, "roles": "cross_platform", "notes": ""}, {"id": "TrueBlood-36506806", "acc": "", "section": "covid_cross_platform", "pathogen": "SARS-CoV-2", "vaccine": "inactivated (likely)", "platform": "inactivated", "species": "human", "tissue": "PBMC", "assay": "scRNA-seq", "n": "", "status": "unverified", "recipe": false, "roles": "", "notes": "TrueBlood 36506806 / 36987861"}, {"id": "GSE131929", "acc": "GSE131929", "section": "outcome_linked", "pathogen": "meningococcus B", "vaccine": "4CMenB (Bexsero) + routine infant schedule", "platform": "protein_adjuvanted", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "253", "status": "discovered", "recipe": true, "roles": "outcome_linked, reactogenicity, age_extremes", "notes": "GEO carries per-subject post-vaccination fever (Fever/No_fever) AND MenB SBA titre"}, {"id": "GSE124533", "acc": "GSE124533", "section": "outcome_linked", "pathogen": "multiple (YF, VZV, HBV, influenza)", "vaccine": "STAMARIL, VARILRIX, ENGERIX-B, AGRIPPAL, FLUAD, PLACEBO", "platform": "multi", "species": "human", "tissue": "whole blood", "assay": "Agilent microarray", "n": "1606 samples / 123 subjects", "status": "discovered", "recipe": true, "roles": "outcome_linked, reactogenicity, cross_platform, placebo_controlled", "notes": "BIOVACSAFE. The single best resource for signature<->adverse-outcome work: a randomised inpatient study with a SALINE PLACEBO arm (n=20), distributing CDISC SDTM clinical domains alongside the arrays - AE (552 MedDRA-coded events with severity, seriousness, causality and onset day), DM (arm, age, sex), VS_SCORED (5,053 temperature readings) and LB (labs). GEO's \"participant\" characteristic matches"}, {"id": "GSE253685", "acc": "GSE253685", "section": "infection_vs_vaccination", "pathogen": "influenza", "vaccine": "seasonal influenza vaccine, then live influenza challenge", "platform": "challenge_model", "species": "human", "tissue": "PBMC", "assay": "Agilent microarray", "n": "339 samples / ~71 subjects", "status": "discovered", "recipe": true, "roles": "infection_vs_vaccination, challenge_model", "notes": "Controlled human influenza challenge with vaccinated (n~36) and unvaccinated (n~35) arms, each with a pre-challenge baseline. The cleanest available answer to \"how does vaccination change the response to infection\": both arms are infected, in one study, on one platform, so vaccination status is the only systematic difference."}, {"id": "GSE201530", "acc": "GSE201530", "section": "infection_vs_vaccination", "pathogen": "SARS-CoV-2 (Omicron BA.1)", "vaccine": "COVID-19 vaccination and/or prior infection", "platform": "multi", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "55 profiled (83 in paper)", "status": "discovered", "recipe": true, "roles": "infection_vs_vaccination, cross_sectional, matched_pair", "notes": "2x2 of prior vaccination x prior infection in acutely Omicron-infected outpatients, plus healthy controls. Cross-sectional: no pre-infection draw per subject, so this is scored with the group-comparison mode against the healthy-control arm rather than the paired machinery. The \"Vaccination, Prior infection\" cell has n=1 and drops out."}, {"id": "GSE172450", "acc": "GSE172450", "section": "infection", "pathogen": "Plasmodium falciparum (malaria)", "vaccine": "none (controlled human malaria infection)", "platform": "infection", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "187 samples / 13 volunteers", "status": "discovered", "recipe": true, "roles": "infection, challenge_model, repeat_exposure", "notes": "Controlled human malaria infection with volunteers re-challenged up to three times, each episode having its own pre-challenge baseline. The episode is encoded as `dose`, so first/second/third infection is directly comparable to prime/boost in the vaccine datasets. T6, diagnosis and memory draws have no fixed day and are dropped."}, {"id": "GSE218157", "acc": "GSE218157", "section": "animal", "pathogen": "tuberculosis (BCG)", "vaccine": "BCG by five routes (IV, ID, AE, HD-ID, ID/AE)", "platform": "live_attenuated_bacterial", "species": "rhesus", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "144 samples / 36 macaques", "status": "discovered", "recipe": true, "roles": "animal, route_comparison, outcome_linked", "notes": "Rhesus macaques vaccinated with BCG by different routes, each animal sampled pre-vaccination then at d2/wk2/wk12, and each carrying a protection outcome from subsequent M. tuberculosis challenge. Expression columns are named <animal>_<runNumber> with no timepoint, so they are paired by sorting each animal's four columns numerically against its four visits in pre/d2/wk2/wk12 order; the numbers run "}, {"id": "GSE87633", "acc": "GSE87633", "section": "animal", "pathogen": "vaccinia virus", "vaccine": "MVA (attenuated), vs virulent WR, vs MVA-then-WR challenge", "platform": "live_attenuated", "species": "mouse", "tissue": "spleen (of 8 tissues deposited)", "assay": "bulk RNA-seq", "n": "374 samples across 8 tissues", "status": "discovered", "recipe": true, "roles": "animal, matched_pair, vaccinate_then_challenge, multi_tissue", "notes": "Another matched vaccine/virus pair: MVA is the attenuated vaccinia strain, WR the virulent one, and MVA7+WR are animals vaccinated then challenged. Each mouse is sampled once, so this is cross-sectional against the uninfected controls, with condition = cohort x day. Restricted here to spleen as the systemic immune organ; the deposit also holds bone marrow, brain, liver, lung, skin, small intestine"}, {"id": "GSE222229", "acc": "GSE222229", "section": "animal", "pathogen": "yellow fever virus", "vaccine": "Stamaril / YF-VAX / vYF, then wild-type Asibi challenge", "platform": "live_attenuated", "species": "cynomolgus", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "164 samples", "status": "discovered", "recipe": true, "roles": "animal, matched_pair, vaccinate_then_challenge", "notes": "Three live attenuated yellow fever vaccines in cynomolgus macaques, followed months later by challenge with wild-type Asibi virus; the Asibi-labelled animals are the unvaccinated challenge controls, sampled only in the challenge phase. This is a matched vaccine/virus pair for one pathogen in one study - the design the human yellow fever data cannot provide. Dose 1 is the vaccination phase (baselin"}, {"id": "GSE243442", "acc": "GSE243442", "section": "infection", "pathogen": "yellow fever virus (wild type)", "vaccine": "none", "platform": "infection", "species": "human", "tissue": "PBMC", "assay": "bulk RNA-seq", "n": "55", "status": "discovered", "recipe": true, "roles": "infection, case_control, matched_pair", "notes": "Acute wild-type yellow fever infection from the 2016-18 Brazilian outbreak, split by survival. This is the matched counterpart to the YF-17D vaccine datasets: YF-17D is the live attenuated form of the same virus, so vaccine and infection can be compared for one pathogen. Cross-sectional, so effect sizes are not comparable with the paired vaccine designs."}, {"id": "GSE34404", "acc": "GSE34404", "section": "infection", "pathogen": "Plasmodium falciparum (malaria)", "vaccine": "none", "platform": "infection", "species": "human", "tissue": "whole blood", "assay": "Illumina microarray", "n": "155 (symptomatic children + age-matched controls)", "status": "discovered", "recipe": true, "roles": "infection, case_control", "notes": ""}, {"id": "GSE282464", "acc": "GSE282464", "section": "infection", "pathogen": "multiple (COVID-19, influenza A/B, sepsis, septic shock, co-infections)", "vaccine": "none", "platform": "infection", "species": "human", "tissue": "whole blood", "assay": "bulk RNA-seq", "n": "377", "status": "discovered", "recipe": false, "roles": "infection, reference_panel, cross_sectional", "notes": "Multi-centre panel across 12 infection types and 5 countries - the best single reference for \"what does infection X look like in blood\". CROSS-SECTIONAL: no pre-infection draw, so the paired machinery does not apply (same limitation as GSE201530). Needs a group-comparison mode. Not yet wired up."}, {"id": "GSE13485", "acc": "GSE13485", "section": "non_covid", "pathogen": "yellow fever virus", "vaccine": "YF-17D", "platform": "live_attenuated", "species": "human", "tissue": "PBMC", "assay": "Affymetrix microarray", "n": "~15-25 adults", "status": "literature", "recipe": false, "roles": "reference", "notes": ""}, {"id": "GSE13486", "acc": "GSE13486", "section": "non_covid", "pathogen": "yellow fever virus", "vaccine": "YF-17D", "platform": "live_attenuated", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "trial 2", "status": "literature", "recipe": true, "roles": "reference", "notes": ""}, {"id": "GSE13699", "acc": "GSE13699", "section": "non_covid", "pathogen": "yellow fever virus", "vaccine": "YF-17D", "platform": "live_attenuated", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "", "status": "literature", "recipe": true, "roles": "reference", "notes": ""}, {"id": "GSE29614", "acc": "GSE29614", "section": "non_covid", "pathogen": "influenza", "vaccine": "TIV 2007-08", "platform": "inactivated", "species": "human", "tissue": "PBMC", "assay": "Affymetrix microarray", "n": "", "status": "literature", "recipe": true, "roles": "reference", "notes": ""}, {"id": "GSE29617", "acc": "GSE29617", "section": "non_covid", "pathogen": "influenza", "vaccine": "TIV 2008-09", "platform": "inactivated", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "", "status": "literature", "recipe": true, "roles": "reference", "notes": ""}, {"id": "GSE29615", "acc": "GSE29615", "section": "non_covid", "pathogen": "influenza", "vaccine": "LAIV (FluMist)", "platform": "live_attenuated", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "", "status": "literature", "recipe": true, "roles": "reference", "notes": ""}, {"id": "GSE29619", "acc": "GSE29619", "section": "non_covid", "pathogen": "influenza", "vaccine": "TIV + LAIV (SuperSeries)", "platform": "multi", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "", "status": "literature", "recipe": false, "roles": "", "notes": "SuperSeries of GSE29614/15/17"}, {"id": "GSE29366", "acc": "GSE29366", "section": "non_covid", "pathogen": "influenza", "vaccine": "TIV", "platform": "inactivated", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "", "status": "literature", "recipe": false, "roles": "", "notes": ""}, {"id": "Franco-2013", "acc": "", "section": "non_covid", "pathogen": "influenza", "vaccine": "TIV", "platform": "inactivated", "species": "human", "tissue": "blood", "assay": "microarray + eQTL", "n": "", "status": "none", "recipe": false, "roles": "", "notes": ""}, {"id": "Furman-2014", "acc": "", "section": "non_covid", "pathogen": "influenza", "vaccine": "TIV", "platform": "inactivated", "species": "human", "tissue": "blood", "assay": "microarray", "n": "", "status": "none", "recipe": false, "roles": "", "notes": ""}, {"id": "Sobolev-2016", "acc": "", "section": "non_covid", "pathogen": "influenza", "vaccine": "AS03-adjuvanted H1N1 (Pandemrix)", "platform": "adjuvanted_split", "species": "human", "tissue": "blood", "assay": "transcriptomics", "n": "", "status": "none", "recipe": false, "roles": "", "notes": ""}, {"id": "Thakar-2015", "acc": "", "section": "non_covid", "pathogen": "influenza", "vaccine": "influenza (older adults)", "platform": "inactivated", "species": "human", "tissue": "blood", "assay": "transcriptomics", "n": "", "status": "none", "recipe": false, "roles": "", "notes": ""}, {"id": "GSE107672", "acc": "GSE107672", "section": "non_covid", "pathogen": "malaria", "vaccine": "RTS", "platform": "protein_adjuvanted", "species": "human", "tissue": "PBMC & whole blood", "assay": "RNA-seq + Affymetrix", "n": "210 subjects", "status": "literature", "recipe": false, "roles": "", "notes": "integrates 5 RTS,S studies; no series matrix, expression in supplementary txt"}, {"id": "RTSS-components", "acc": "GSE103401, GSE102288, GSE89292, GSE103862, GSE103874", "section": "non_covid", "pathogen": "malaria", "vaccine": "RTS", "platform": "protein_adjuvanted", "species": "human", "tissue": "PBMC / whole blood", "assay": "RNA-seq / microarray", "n": "", "status": "literature", "recipe": false, "roles": "", "notes": ""}, {"id": "E-MTAB-4629", "acc": "E-MTAB-4629", "section": "non_covid", "pathogen": "malaria", "vaccine": "RTS", "platform": "protein_adjuvanted", "species": "human", "tissue": "blood", "assay": "transcriptomics", "n": "", "status": "literature", "recipe": false, "roles": "", "notes": ""}, {"id": "Moncunill-RTSS", "acc": "", "section": "non_covid", "pathogen": "malaria", "vaccine": "RTS", "platform": "protein_adjuvanted", "species": "human", "tissue": "blood", "assay": "transcriptomics", "n": "", "status": "none", "recipe": false, "roles": "", "notes": ""}, {"id": "GSE124217", "acc": "GSE124217", "section": "non_covid", "pathogen": "tuberculosis", "vaccine": "BCG", "platform": "live_attenuated_bacterial", "species": "human", "tissue": "PBMC", "assay": "transcriptomics", "n": "300BCG cohort", "status": "literature", "recipe": false, "roles": "trained_immunity", "notes": ""}, {"id": "GSE124218", "acc": "GSE124218", "section": "non_covid", "pathogen": "tuberculosis", "vaccine": "BCG", "platform": "live_attenuated_bacterial", "species": "human", "tissue": "PBMC / progenitors", "assay": "transcriptomics", "n": "", "status": "literature", "recipe": false, "roles": "trained_immunity", "notes": ""}, {"id": "Rechtien-2017", "acc": "", "section": "non_covid", "pathogen": "ebola", "vaccine": "rVSV-ZEBOV", "platform": "live_recombinant_vector", "species": "human", "tissue": "blood", "assay": "transcriptomics", "n": "", "status": "none", "recipe": false, "roles": "", "notes": ""}, {"id": "GSE125860", "acc": "GSE125860", "section": "non_covid", "pathogen": "hepatitis B", "vaccine": "HEPLISAV vs Engerix-B", "platform": "protein_adjuvanted", "species": "human", "tissue": "blood", "assay": "transcriptomics", "n": "", "status": "literature", "recipe": false, "roles": "", "notes": ""}, {"id": "Zoster-NCT", "acc": "NCT01331161, NCT04047979", "section": "non_covid", "pathogen": "varicella-zoster", "vaccine": "ZOSTAVAX + SHINGRIX", "platform": "multi", "species": "human", "tissue": "blood", "assay": "transcriptomics", "n": "", "status": "none", "recipe": false, "roles": "", "notes": "trial registrations only; deposited GEO/SDY to locate"}, {"id": "Li-2014", "acc": "", "section": "non_covid", "pathogen": "meningococcus / pneumococcus", "vaccine": "Menactra", "platform": "polysaccharide / conjugate", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "", "status": "literature", "recipe": false, "roles": "", "notes": "signatures as MSigDB LI_PBMC_* sets"}, {"id": "GSE124689", "acc": "GSE124689", "section": "prereg_holdout", "pathogen": "influenza", "vaccine": "FLUAD (MF59-adjuvanted TIV)", "platform": "adjuvanted_split", "species": "human", "tissue": "whole blood", "assay": "Agilent microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": ""}, {"id": "GSE124842", "acc": "GSE124842", "section": "prereg_holdout", "pathogen": "tetanus/diphtheria/pertussis", "vaccine": "Boostrix (alum-adsorbed dTpa)", "platform": "protein_adjuvanted", "species": "human", "tissue": "whole blood", "assay": "Agilent microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": ""}, {"id": "GSE124719", "acc": "GSE124719", "section": "prereg_holdout", "pathogen": "hepatitis B / influenza", "vaccine": "Fendrix (AS04 HBV) and FLUAD", "platform": "multi", "species": "human", "tissue": "whole blood (muscle biopsies excluded)", "assay": "Agilent microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": ""}, {"id": "GSE48018", "acc": "GSE48018", "section": "prereg_holdout", "pathogen": "influenza", "vaccine": "trivalent inactivated influenza (unadjuvanted)", "platform": "inactivated", "species": "human", "tissue": "whole blood", "assay": "Illumina microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": ""}, {"id": "GSE48762", "acc": "GSE48762", "section": "prereg_holdout", "pathogen": "influenza / pneumococcus", "vaccine": "Fluzone (TIV) and Pneumovax", "platform": "multi", "species": "human", "tissue": "whole blood (venous draws only)", "assay": "Illumina microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": "Vaccine labels in the deposit are inconsistent (FLUZONE / Flu / Influenza; PNEUM / Pneumovax; NS / Saline / saline), so arms are matched by regex. Finger-stick samples are excluded to keep one blood compartment. Day 0 is the baseline; the day -168 and -7 draws do not match a visit pattern and are dropped."}, {"id": "GSE73072", "acc": "GSE73072", "section": "prereg_holdout", "pathogen": "influenza / rhinovirus / RSV", "vaccine": "none - deliberate challenge with replication-competent virus", "platform": "infection", "species": "human", "tissue": "peripheral blood", "assay": "Affymetrix microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": "Timepoints are hours, converted to days. Hour 0 is the baseline; negative hours are dropped."}, {"id": "GSE90732", "acc": "GSE90732", "section": "prereg_holdout", "pathogen": "influenza", "vaccine": "none - H1N1 challenge", "platform": "infection", "species": "human", "tissue": "blood", "assay": "Illumina microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": ""}, {"id": "GSE82152", "acc": "GSE82152", "section": "prereg_holdout", "pathogen": "yellow fever", "vaccine": "YF-17D (live attenuated)", "platform": "live_attenuated", "species": "human", "tissue": "PBMC", "assay": "microarray", "n": "", "status": "holdout", "recipe": true, "roles": "", "notes": "Nine dose groups are the same vaccine and are pooled into one arm, per AMENDMENT-001."}], "processed": [{"id": "GSE124533", "pathogen": "multiple (YF, VZV, HBV, influenza)", "species": "human", "vaccine": "STAMARIL, VARILRIX, ENGERIX-B, AGRIPPAL, FLUAD, PLACEBO", "design": "paired", "subjects": 146, "samples": 1460, "genes": 20141, "modules": 344, "groups": ["AGRIPPAL", "ENGERIXB1", "ENGERIXB3", "FLUADC", "PLACEBOAB1C", "PLACEBOB3", "STAMARIL", "VARILRIX"]}, {"id": "GSE124689", "pathogen": "influenza", "species": "human", "vaccine": "FLUAD (MF59-adjuvanted TIV)", "design": "paired", "subjects": 114, "samples": 568, "genes": 20141, "modules": 344, "groups": ["FLUADD"]}, {"id": "GSE124719", "pathogen": "hepatitis B / influenza", "species": "human", "vaccine": "Fendrix (AS04 HBV) and FLUAD", "design": "paired", "subjects": 30, "samples": 60, "genes": 20141, "modules": 344, "groups": ["FENDRIXE", "FLUADE"]}, {"id": "GSE124842", "pathogen": "tetanus/diphtheria/pertussis", "species": "human", "vaccine": "Boostrix (alum-adsorbed dTpa)", "design": "paired", "subjects": 200, "samples": 999, "genes": 20141, "modules": 344, "groups": ["BOOSTRIX"]}, {"id": "GSE131929", "pathogen": "meningococcus B", "species": "human", "vaccine": "4CMenB (Bexsero) + routine infant schedule", "design": "paired", "subjects": 129, "samples": 253, "genes": 13493, "modules": 255, "groups": ["all"]}, {"id": "GSE13486", "pathogen": "yellow fever virus", "species": "human", "vaccine": "YF-17D", "design": "paired", "subjects": 25, "samples": 87, "genes": 14386, "modules": 338, "groups": ["all"]}, {"id": "GSE13699", "pathogen": "yellow fever virus", "species": "human", "vaccine": "YF-17D", "design": "paired", "subjects": 27, "samples": 124, "genes": 17445, "modules": 345, "groups": ["all"]}, {"id": "GSE169159", "pathogen": "SARS-CoV-2", "species": "human", "vaccine": "BNT162b2", "design": "paired", "subjects": 32, "samples": 181, "genes": 12819, "modules": 269, "groups": ["all"]}, {"id": "GSE190001", "pathogen": "SARS-CoV-2", "species": "human", "vaccine": "BNT162b2 + mRNA-1273", "design": "paired", "subjects": 23, "samples": 386, "genes": 14778, "modules": 279, "groups": ["all"]}, {"id": "GSE201530", "pathogen": "SARS-CoV-2 (Omicron BA.1)", "species": "human", "vaccine": "COVID-19 vaccination and/or prior infection", "design": "cross_sectional", "subjects": 54, "samples": 54, "genes": 13536, "modules": 274, "groups": ["Omicron, immunologically naive", "Omicron, vaccinated", "control", "Omicron, prior infection"]}, {"id": "GSE201533", "pathogen": "SARS-CoV-2", "species": "human", "vaccine": "ChAdOx1 / BNT162b2", "design": "paired", "subjects": 55, "samples": 161, "genes": 13020, "modules": 269, "groups": ["BNT|II", "ChAd|I", "ChAd|II"]}, {"id": "GSE218157", "pathogen": "tuberculosis (BCG)", "species": "rhesus", "vaccine": "BCG by five routes (IV, ID, AE, HD-ID, ID/AE)", "design": "paired", "subjects": 36, "samples": 144, "genes": 15776, "modules": 334, "groups": ["AE", "HD-ID", "ID", "ID/AE", "IV"]}, {"id": "GSE220682", "pathogen": "SARS-CoV-2", "species": "human", "vaccine": "BNT162b2", "design": "paired", "subjects": 90, "samples": 106, "genes": 13027, "modules": 256, "groups": ["all"]}, {"id": "GSE222229", "pathogen": "yellow fever virus", "species": "cynomolgus", "vaccine": "Stamaril / YF-VAX / vYF, then wild-type Asibi challenge", "design": "paired", "subjects": 24, "samples": 164, "genes": 9507, "modules": 255, "groups": ["Asibi", "Stamaril", "YF-VAX", "vYF"]}, {"id": "GSE243442", "pathogen": "yellow fever virus (wild type)", "species": "human", "vaccine": "none", "design": "cross_sectional", "subjects": 55, "samples": 55, "genes": 15692, "modules": 309, "groups": ["YF acute (fatal)", "YF acute (survived)", "control"]}, {"id": "GSE253685", "pathogen": "influenza", "species": "human", "vaccine": "seasonal influenza vaccine, then live influenza challenge", "design": "paired", "subjects": 71, "samples": 335, "genes": 18406, "modules": 345, "groups": ["Unvaccinated", "Vaccinated"]}, {"id": "GSE29614", "pathogen": "influenza", "species": "human", "vaccine": "TIV 2007-08", "design": "paired", "subjects": 9, "samples": 27, "genes": 19494, "modules": 345, "groups": ["all"]}, {"id": "GSE29615", "pathogen": "influenza", "species": "human", "vaccine": "LAIV (FluMist)", "design": "paired", "subjects": 28, "samples": 83, "genes": 18321, "modules": 345, "groups": ["all"]}, {"id": "GSE29617", "pathogen": "influenza", "species": "human", "vaccine": "TIV 2008-09", "design": "paired", "subjects": 28, "samples": 80, "genes": 18321, "modules": 345, "groups": ["all"]}, {"id": "GSE34404", "pathogen": "Plasmodium falciparum (malaria)", "species": "human", "vaccine": "none", "design": "cross_sectional", "subjects": 155, "samples": 155, "genes": 20515, "modules": 345, "groups": ["malaria", "control"]}, {"id": "GSE48018", "pathogen": "influenza", "species": "human", "vaccine": "trivalent inactivated influenza (unadjuvanted)", "design": "paired", "subjects": 116, "samples": 431, "genes": 18736, "modules": 345, "groups": ["all"]}, {"id": "GSE48762", "pathogen": "influenza / pneumococcus", "species": "human", "vaccine": "Fluzone (TIV) and Pneumovax", "design": "paired", "subjects": 31, "samples": 197, "genes": 18759, "modules": 345, "groups": ["influenza", "pneumovax"]}, {"id": "GSE73072", "pathogen": "influenza / rhinovirus / RSV", "species": "human", "vaccine": "none - deliberate challenge with replication-competent virus", "design": "paired", "subjects": 148, "samples": 2741, "genes": 10823, "modules": 334, "groups": ["H1N1", "H3N2", "HRV", "RSV"]}, {"id": "GSE82152", "pathogen": "yellow fever", "species": "human", "vaccine": "YF-17D (live attenuated)", "design": "paired", "subjects": 21, "samples": 109, "genes": 18404, "modules": 343, "groups": ["all"]}, {"id": "GSE87633", "pathogen": "vaccinia virus", "species": "mouse", "vaccine": "MVA (attenuated), vs virulent WR, vs MVA-then-WR challenge", "design": "cross_sectional", "subjects": 51, "samples": 51, "genes": 12698, "modules": 305, "groups": ["Uninfected d0", "MVA d0.5", "MVA d1.5", "MVA d3", "MVA d5", "MVA7+WR d5", "MVA7+WR d3", "WR d1.5", "WR d0.5", "WR d3", "WR d5", "MVA7+WR d0.5", "MVA7+WR d1.5"]}, {"id": "GSE90732", "pathogen": "influenza", "species": "human", "vaccine": "none - H1N1 challenge", "design": "paired", "subjects": 21, "samples": 108, "genes": 20515, "modules": 345, "groups": ["all"]}], "adjuvant": [{"arm": "PLACEBOAB1C", "adjuvant": "saline (control)", "study": "GSE124533", "day": 1.0, "n": 20, "cell_cycle": -0.001, "inflammation": 0.05, "interferon": 0.071, "plasmablast": -0.003}, {"arm": "ENGERIXB1", "adjuvant": "aluminium salt", "study": "GSE124533", "day": 1.0, "n": 21, "cell_cycle": 0.043, "inflammation": 0.103, "interferon": 0.098, "plasmablast": 0.021}, {"arm": "ENGERIXB3", "adjuvant": "aluminium salt", "study": "GSE124533", "day": 1.0, "n": 20, "cell_cycle": 0.034, "inflammation": 0.063, "interferon": 0.003, "plasmablast": -0.005}, {"arm": "BOOSTRIX", "adjuvant": "aluminium salt", "study": "GSE124842", "day": 1.0, "n": 200, "cell_cycle": -0.031, "inflammation": 0.128, "interferon": 0.226, "plasmablast": -0.054}, {"arm": "FENDRIXE", "adjuvant": "AS04 (aluminium + MPL)", "study": "GSE124719", "day": 1.0, "n": 3, "cell_cycle": -0.067, "inflammation": 0.07, "interferon": 0.009, "plasmablast": -0.051}, {"arm": "AGRIPPAL", "adjuvant": "none (inactivated)", "study": "GSE124533", "day": 1.0, "n": 21, "cell_cycle": -0.008, "inflammation": 0.085, "interferon": 0.219, "plasmablast": -0.019}, {"arm": "FLUADC", "adjuvant": "MF59 (squalene)", "study": "GSE124533", "day": 1.0, "n": 20, "cell_cycle": -0.055, "inflammation": 0.32, "interferon": 0.686, "plasmablast": -0.114}, {"arm": "FLUADD", "adjuvant": "MF59 (squalene)", "study": "GSE124689", "day": 1.0, "n": 114, "cell_cycle": -0.066, "inflammation": 0.343, "interferon": 0.843, "plasmablast": -0.156}, {"arm": "FLUADE", "adjuvant": "MF59 (squalene)", "study": "GSE124719", "day": 1.0, "n": 3, "cell_cycle": -0.155, "inflammation": 0.387, "interferon": 0.924, "plasmablast": -0.138}, {"arm": "VARILRIX", "adjuvant": "none (live)", "study": "GSE124533", "day": 1.0, "n": 20, "cell_cycle": -0.002, "inflammation": 0.098, "interferon": 0.14, "plasmablast": -0.028}, {"arm": "STAMARIL", "adjuvant": "none (live, d7)", "study": "GSE124533", "day": 7.0, "n": 20, "cell_cycle": 0.026, "inflammation": 0.116, "interferon": 1.239, "plasmablast": -0.076}], "prereg": {"osf": "https://osf.io/86t3u/overview", "h1": "INCONCLUSIVE", "h2": "INCONCLUSIVE", "h1_detail": {"arms_included": 6, "required": 8, "fisher_p": 0.4, "nonrep_early": "3/4", "rep_late": "2/2"}, "h2_detail": {"tests": 12, "required": 20, "g95": 1.01, "frac_sig": 0.0}}}