Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Characterization of the placental macrophage secretome: implications for antiviral activity.
PMID 19070362 · PMC2947718 · Placenta · 2009 · 7 claims · 5 setups
PM and MDM secrete different soluble proteins, some of which may contribute to decreased HIV-1 replication in PM
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Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.
PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups
HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162
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Has reproduction · 90
Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts.
PMID 39959292 · PMC11825298 · Bio-protocol · 2025 · 7 claims · 6 setups
Mapping adapter-trimmed reads first to the pathogen genome recovers more pathogen reads than the traditional host-first mapping approach.
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Transcriptome annotation using tandem SAGE tags.
PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups
A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)
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Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.
PMID 18951626 · PMC3867668 · Placenta · 2008 · 6 claims · 6 setups
Placental macrophages support significantly lower HIV-1 replication than monocyte-derived macrophages
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Has reproduction · 64
Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.
PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 7 claims · 8 setups
A distinct subset of COL6A3+ tumor-associated fibroblasts (TAFs) with matrix-fibroblast characteristics exists in GBM and is significantly enriched in non-responders to neoadjuvant combination therapy.
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Has reproduction · 85
Protocol for transcriptomic and epigenomic analysis of JAK inhibitor sensitivity in IFN-γ-primed human macrophages using ATAC-seq and RNA-seq.
PMID 41313685 · PMC12702366 · STAR protocols · 2025 · 7 claims · 7 setups
Integrated ATAC-seq and RNA-seq protocol to profile JAK inhibitor sensitivity in IFN-γ-primed human macrophages
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Has reproduction · 83
Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.
PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups
Mural cell-derived chemokines CCL2 and MIF preserve vascular macrophage survival and homeostatic function, generating a protective niche.
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Has reproduction · 86
Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.
PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups
RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.
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Has reproduction · 67
Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.
PMID 34795257 · PMC8602323 · Nature communications · 2021 · 8 claims · 12 setups
PYK2 was identified as a putative IRF5 kinase via a kinase inhibitor library screen in macrophages
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Malarial hemozoin activates the NLRP3 inflammasome through Lyn and Syk kinases.
PMID 19696895 · PMC2722371 · PLoS pathogens · 2009 · 7 claims · 8 setups
Hemozoin induces IL-1β maturation and secretion in an NLRP3-, ASC- and caspase-1-dependent, but NLRC4-independent, manner
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Has reproduction · 70
MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.
PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups
MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling
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Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups
CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.
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Has reproduction · 90
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.
PMID 37012480 · PMC10172113 · Nature methods · 2023 · 8 claims · 5 setups
pSCoPE (prioritized precursor selection via MaxQuant.Live) increases sensitivity, data completeness, and proteome coverage more than twofold over shotgun single-cell proteomics
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Has reproduction · 48
Screening of Diagnostic Biomarkers and Immune Infiltration Characteristics Linking Rheumatoid Arthritis and Rosacea Based on Bioinformatics Analysis.
PMID 39104909 · PMC11299729 · Journal of inflammation research · 2024 · 8 claims · 8 setups
277 co-expressed DEGs shared between RA and rosacea are enriched in immune processes and chemokine-mediated signaling pathways
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Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity
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Has reproduction · 63
Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.
PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups
The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.
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Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.
PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups
Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis
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A homozygous CARD9 mutation in a family with susceptibility to fungal infections.
PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups
A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.