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).

• Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

  PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups

  Has reproduction · 69

  Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis

  colon gut single-cell 16s western

• Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution.

  PMID 41513700 · PMC12891662 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Cytomix (TNFɑ+IFNɣ+IL1β) treatment of human colon organoids best recapitulates molecular features of human IBD compared to DSS or irradiation injury models.

  colon cytomix-treated scrna-seq immunofluorescence activated

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• Resolving clonal evolution and selection of extrachromosomal DNA at single-cell resolution.

  PMID 41606654 · PMC12853921 · Genome biology · 2026 · 7 claims · 8 setups

  Full-text index only

  ecSingle, a computational method integrating allelic imbalance (BAF deviation) and outlier expression from scRNA-seq, can identify oncogene-carrying ecDNA at single-cell resolution.

  colo320dm glioblastoma medulloblastoma ce26 scrna-seq whole-genome long-read

• Notch3 regulates pericyte phenotypic plasticity in colorectal cancer.

  PMID 41618002 · PMC12960917 · Communications biology · 2026 · 8 claims · 8 setups

  Full-text index only

  Murine tumor pericytes originate from normal tissue-resident pericytes that proliferate inside tumors

  aom crc pdgfrβ-creert2 notch3-creert2 scrna-seq facs lineage

• Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

  PMID 41566530 · PMC12906006 · Genome biology · 2026 · 7 claims · 6 setups

  Full-text index only

  Pseudobulk and real bulk RNA-seq deconvolution performance differ significantly, and method ranking consistency is lower between pseudobulk and real bulk than within either data type alone

  breast real colon tcga paired pseudobulk bulk

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• Bidirectional CRISPR screens decode a GLIS3-dependent fibrotic cell circuit.

  PMID 41501466 · PMC12820784 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  Inflammation-associated fibroblasts (IAFs), induced by proinflammatory FCN1+IL1B+ macrophages, produce profibrotic IL-11 and drive fibrosis in IBD

  intestinal colon pdgfra+ colonic scrna-seq xenium masson's

• Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

  PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

  Full-text index only

  BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

  colorectal colon patients bulk single-cell spatial bulk

• Identification of Poor Prognosis-Associated Fibroblast Subpopulation Signature Genes Utilizing the Scissor Algorithm to Classify Colorectal Cancer Subtypes and Evaluate the Immune Landscape.

  PMID 41787974 · PMC13180509 · Gut and liver · 2026 · 8 claims · 8 setups

  Full-text index only

  Scissor+ fibroblast subpopulations significantly correlated with prognosis were identified in CRC using the Scissor algorithm integrating scRNA-seq, bulk RNA-seq, and clinical data

  tcga gse39582 gse166555 scrna-seq bulk single-cell cell-cell

• Machine learning-driven transcriptomic and single-cell profiling of programed cell death patterns in colon cancer.

  PMID 41854308 · PMC13009810 · Science progress · 2026 · 8 claims · 8 setups

  Full-text index only

  Disulfidptosis and anoikis are consistently identified as the most robust prognostic PCD patterns in colon cancer across six independent machine learning algorithms

  colon coad ssgsea-based machine differential

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 45

  Eight distinct T cell populations can be identified from CRC tumor tissue by unsupervised clustering of scRNA-seq data

  tumor-infiltrating peripheral cd4+ tumor single-cell unsupervised pearson

• Paneth cell SIRT1 deficiency increases intestinal stress resistance by modulating the gut microbiota.

  PMID 41826553 · PMC13076647 · EMBO reports · 2026 · 8 claims · 8 setups

  Full-text index only

  Generated a novel Paneth-cell-specific SIRT1 knockout mouse model (SIRT1 PKO, Sirt1 f/f;Defa6-Cre+)

  small immune facs-sorted ileum single-cell facs qpcr

• MafB is a conserved transcriptional regulator of macrophage development and functional identity across tissues and species.

  PMID 41759510 · PMC7618887 · Immunity · 2026 · 8 claims · 8 setups

  Full-text index only

  MafB is required for full differentiation of bone-marrow-derived macrophages (BMDMs) in vitro and for development of most RTMs in vivo

  bmdms peritoneal rtms irradiated bulk hashtag-barcoded intracellular

• CSsingle: a unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references.

  PMID 42080261 · PMC13136905 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  CSsingle explicitly corrects for cell-type-specific RNA content (cell size) differences using ERCC spike-ins or a novel computational estimator

  blood breast developing colorectal bulk scrna-seq spatial

• Tachykinin signaling defines distinct populations of glia in the enteric nervous system.

  PMID 41512855 · PMC12832054 · Neuron · 2026 · 8 claims · 8 setups

  Full-text index only

  Mucosal and muscularis glia are transcriptionally distinct populations, with mucosal glia resembling microglia and muscularis glia resembling satellite glia/astrocytes

  ileum gfp+ intestinal intestine bulk scrna-seq bayesprism

• SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.

  PMID 41691474 · PMC13042402 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  SiCmiR, a two-layer neural network, predicts mature miRNA expression profiles from only 977 LINCS L1000 landmark genes

  tcga k562 pancreatic acth-secreting paired bulk scrna-seq-based

• Genetic evidence supporting obesity as a risk factor for lung squamous cell carcinoma and the identification of MFAP1 as a shared genetic target.

  PMID 41820721 · PMC13096280 · Discover oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  BMI and LUSC show a significant positive genome-wide genetic correlation, robust to constrained-intercept sensitivity analysis and replicated by GNOVA.

  gwas gtex scrna-seq ldsc gnova ρ-hess