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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Has reproduction · 43
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.
PMID 34089405 · PMC8179884 · Rice (New York, N.Y.) · 2021 · 8 claims · 7 setups
N22 performs better under dual (low N + low water) stress owing to better root architecture, chlorophyll/porphyrin synthesis and oxidative stress management
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Has reproduction · 88
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.
PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups
COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.
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Has reproduction · 93
7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress.
PMID 39952919 · PMC11828898 · Nature communications · 2025 · 8 claims · 8 setups
Heat shock induces de novo transcription and nuclear accumulation of 7SL RNA together with SRP proteins, which then bind chromatin at promoters
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Has reproduction · 100
Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.
PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups
iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action
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Has reproduction · 53
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.
PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 6 setups
spliceJAC quantifies multivariate mRNA splicing from unspliced/spliced count matrices to construct cell state-specific gene-gene (Jacobian) interaction matrices.
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Has reproduction · 78
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups
CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.
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Has reproduction · 84
Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.
PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
TEPs in NSCLC show 111 upregulated and 108 downregulated genes versus non-cancer control platelets, enriched in ECM interaction, cytoskeleton, immune signaling, and platelet activation pathways.
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Has reproduction · 69
COVID-19 vaccination atlas using an integrative systems vaccinology approach.
PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups
mRNA vaccines induce transient but strong immune responses after booster doses
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Has reproduction · 50
huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.
PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups
huSA is a publicly accessible database integrating data from 17 skin diseases and 63 independent datasets, including 1434 scRNA-seq, 63 spatial transcriptomics, and 1502 bulk RNA-seq samples
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Has reproduction · 33
To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.
PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups
C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 50
Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.
PMID 36450262 · PMC9792173 · Cell reports · 2022 · 7 claims · 7 setups
Following transient CD4 depletion, IL-21-producing Tfh cells do repopulate but are outnumbered by immunomodulatory CD4 T cells (Tregs, Th17), and IL-21+ frequency remains low within activated CD4 T cells.
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Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.
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Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.
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Has reproduction · 50
The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.
PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups
Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants