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).

• 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

  Has reproduction · 50

  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

  skin scrna-seq single prurigo scrna-seq bulk spatial

• 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

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 7 setups

  Has reproduction · 75

  CLAD harbors disease-specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 ffpe end-stage single-cell single-nucleus integrative

• A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.

  PMID 39744938 · PMC11684814 · The Journal of clinical investigation · 2025 · 8 claims · 4 setups

  Has reproduction · 78

  Integration of public and newly generated scRNA-seq datasets yields a compendium of 139 subjects (193 samples, 403,973 immune cells) spanning CSF and blood across healthy controls and multiple neurologic diseases.

  csf scrna-seq trajectory flow

• Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.

  PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 6 setups

  Has reproduction · 30

  A core set of 60 genes captures a continuous pseudotemporal disease axis from control to PD GBA-N370S iPSC-derived dopamine neurons (52 downregulated, 8 upregulated).

  facs-purified facs-sorted ipsc ipsc-derived bulk single-cell facs

• Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

  PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

  Has reproduction · 55

  Microglia, endothelial cells, and pericytes exhibit the highest type I interferon (IFN-I) activity among PD midbrain cell types, with microglia showing markedly higher activity in PD.

  midbrain microglia substantia mptp-induced single-cell gene bulk

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.

  grch38 homogeneous per single single-cell clustering cell-type

• Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.

  PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  Reanalysis of scRNA-Seq identified 279 iMSC signature genes upregulated in BM MSCs of MM patients vs healthy donors, covering 82% of the top 50 previously defined iMSC genes

  facs-isolated mscs expanded single-cell bulk meta-analysis

• Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

  PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

  Full-text index only

  AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

  entorhinal subjects expression differentially microarray significance principal

• Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

  PMID 41758938 · PMC12947870 · Science advances · 2026 · 7 claims · 8 setups

  Has reproduction · 84

  MYOD1 L122R-mutant SRMS comprises three coexisting tumor cell states (MYOD1-enriched progenitor-like, proliferative transition, and partially differentiated with reduced MYOD1 activity) reflecting disrupted myogenic differentiation.

  six myod1 independent paired single-nucleus targeted bulk

• An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

  PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

  oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor

• Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.

  PMID 35951114 · PMC9372016 · Cellular and molecular life sciences : CMLS · 2022 · 8 claims · 8 setups

  Has reproduction · 98

  Coordinated gene expression patterns across cell types are disrupted and re-organized by mTBI with distinct regional, cellular, and temporal (24-h vs 7-day) specificity.

  hippocampus frontal peripheral cell-type single-cell svm-based ligand-receptor

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral

• The liver as an immunological barrier redefined by single-cell analysis.

  PMID 32176810 · PMC7218664 · Immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 100

  Single-cell RNA-seq enables unbiased characterization of liver cell states, developmental trajectories and rare immune populations that bulk averaging obscures, redefining liver cell-type mapping.

  c57bl liver whole-liver hepatocytes scrna-seq facs-based plate-based

• Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

  PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups

  Has reproduction · 53

  A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.

  metastatic top breast tnbc single-cell functional mutational

• Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

  PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

  Full-text index only

  Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

  peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning

• Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

  PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

  post-mortem brain zebrafish bulk single-cell unsupervised

• Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.

  PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 6 claims · 7 setups

  Has reproduction · 100

  A distinct gene co-expression module with a prominent T cell signature is enriched in unstable plaques and distinguishes high-risk from low-risk lesions.

  carotid calcified atherosclerotic cell-specific microarray single-cell loss-of-function

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

  peripheral leukocytes plasma degs bulk single-cell plasma

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor