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).

• 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

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

  Has reproduction · 85

  Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

  normal er+ epithelial malignant single-cell spatial copy

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 6 setups

  Has reproduction · 90

  A single-nucleus transcriptomic atlas of 37 human sural nerves (365,708 nuclei) defines 24 cell clusters and reveals unexpected heterogeneity of perineurial cells (periC1-3).

  sural rodent single-nucleus subcellular immunofluorescence

• 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

• 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

  Has reproduction · 64

  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.

  newly glioma ffpe tafs single-cell spatial bulk

• 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

• 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

• Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

  PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

  Has reproduction

  SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

  dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial

• 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

• D2H2: diabetes data and hypothesis hub.

  PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 5 setups

  Has reproduction

  D2H2 is a web portal hosting hundreds of curated, uniformly reprocessed diabetes-relevant transcriptomics datasets from GEO with per-study visualization, differential expression, and single-gene queries.

  obese type pubmed bulk single-cell single-gene

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

  PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

  Has reproduction · 50

  Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

  hnscc tcga-hnscc caf fibroblast single-cell bulk spatial

• Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

  PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

  interscapular ibat bat single-nucleus qpcr western

• Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

  PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 76

  DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples

  fresh matched archived dsrct scrna-seq single-nucleus bulk

• CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

  PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 8 setups

  Has reproduction · 42

  CanCellCap, a multi-domain learning framework integrating domain adversarial learning and Mixture of Experts, identifies cancer cells across all tissues, cancers, and sequencing platforms by extracting tissue-common and tissue-specific gene expression patterns.

  testing datasets tisch2 prostate scrna-seq simulated spatial

• Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data.

  PMID 33575569 · PMC7671354 · NAR genomics and bioinformatics · 2020 · 8 claims · 5 setups

  Has reproduction · 61

  Omics Playground is a user-friendly, interactive self-service bioinformatics platform for in-depth analysis, visualization and interpretation of transcriptomics and proteomics data without coding

  transcriptomics contrast rna-seq lc-ms single-cell

• Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.

  PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 61

  Twelve HIA-related genes were identified that are transcriptionally activated by HIFs and functionally implicated in angiogenesis in CRC.

  hct116 crc huvecs chip-seq bulk single-cell

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

  PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 7 setups

  Has reproduction

  A ResNet classifier built on a 10-gene metabolic signature distinguishes all thyroid cancer differentiation states with ~92.7% average accuracy.

  fuscc epithelial aggregated untargeted whole-exome bulk