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).

• Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer.

  PMID 41723121 · PMC12932787 · Nature communications · 2026 · 8 claims · 8 setups

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  Different tumor cell transcriptomic states organize into distinct spatial clusters, or 'villages', each supported by a unique surrounding microenvironment

  liver malignant non-malignant tumor single-cell immunofluorescence non-negative

• Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

  PMID 41388990 · PMC12776951 · The Plant cell · 2026 · 8 claims · 6 setups

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  MERFISH was successfully optimized for wheat inflorescence tissue, enabling localization of a 200-gene panel to cellular resolution across 4 developmental stages

  microdissected cryosectioned wheat merfish-imaged bulk merfish single-nucleus

• Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

  PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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  The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

  first-trimester decidual spots dnk 10x h&e type

• 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

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

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

  Has reproduction · 100

  A distinct gene co-expression module with a prominent T cell signature is associated with unstable plaques.

  carotid calcified atherosclerotic cell-specific microarray single-cell immunohistochemistry

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups

  Has reproduction · 78

  INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

  testis young testicular invade-seq histology sperm

• 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-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model.

  PMID 36321803 · PMC9708074 · eLife · 2022 · 7 claims · 5 setups

  Has reproduction · 72

  Follicle cell-specific Lgl knockdown (Lgl-KD) causes loss of apical-basal polarity and invasive multilayering of the follicular epithelium without long-distance metastasis

  drosophila single-cell bulk immunofluorescence

• Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.

  PMID 41356191 · PMC12680593 · Theranostics · 2026 · 6 claims · 8 setups

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  Berberine enhances energy metabolism (oxidative phosphorylation, ATP biosynthesis, fatty acid metabolism) in intestinal epithelial cells of DSS-induced mice, preserving normal physiological function

  colon feces serum dss-induced single-cell targeted 16s

• Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial.

  PMID 41484096 · PMC12852688 · Nature communications · 2026 · 8 claims · 8 setups

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  Autologous CD133+ BMDSC therapy is safe and well tolerated in AS patients, with no treatment-related serious adverse events over 15-month follow-up

  patients endometrial cd133+ vaginal hysteroscopy digital

• Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

  PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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  APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

  urothelial urothelial-specific ureter hek293t single-cell poly fluorescence

• 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

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

  colorectal colon patients bulk single-cell spatial bulk

• Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment.

  PMID 41556506 · PMC12818872 · eLife · 2026 · 8 claims · 8 setups

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  Mouse TM contains three molecularly distinct, reproducible cell subtypes (TM1, TM2, TM3) identified by scRNA-seq and validated by IF/ISH

  limbal lmx1b scrna-seq snatac-seq immunofluorescence

• Clonal CD8(+) T cells populate the leptomeninges and coordinate with immune cells in human degenerative brain diseases.

  PMID 41593242 · PMC12864034 · Nature immunology · 2026 · 8 claims · 6 setups

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  The human leptomeninges harbor substantial numbers of clonally expanded, tissue-resident memory CD8 T cells (ZNF683-high, CXCR6+, PD-1+)

  postmortem leptomeninges scrna-seq-derived leptomeningeal single-cell flow imaging

• Single-cell transcriptomics reveals keratinocyte dynamic processes associated with S100a4 expression in psoriasiform dermatitis.

  PMID 41660613 · PMC12876221 · Frontiers in immunology · 2025 · 7 claims · 8 setups

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  S100a4 knockout mice show significant pathological improvement in psoriasis-like lesions, including reduced inflammatory cell infiltration and decreased epidermal hyperplasia

  c57bl skin dorsal dcmo crispr western imiquimod-induced

• Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

  PMID 41771574 · PMC12951371 · Cancer genomics & proteomics · 2026 · 7 claims · 8 setups

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  Malignant cells from HCC tumors resolve into six transcriptionally distinct subpopulations, including a progenitor-like CSC subset expressing EPCAM, SOX9, and SOX4

  malignant tumor csc six single-cell spatial copy

• Dynamic transcriptomic remodeling in grafted human neural progenitor cells uncovers mechanisms for vision preservation in a rat model of retinitis pigmentosa.

  PMID 41792118 · PMC12966429 · Nature communications · 2026 · 8 claims · 7 setups

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  Grafted hNPCs primarily differentiate into an astroglial phenotype and mature over time in the degenerative retinal environment

  grafted rcs hnpcs single-cell electroretinography immunofluorescence

• CCL3+ Neutrophil Signature Predicts Response to Neoadjuvant Toripalimab plus Chemotherapy in Patients with Hypopharyngeal Squamous Cell Carcinoma: A Phase II Trial.

  PMID 41817286 · PMC13223550 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 7 claims · 8 setups

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  A proinflammatory, CCL3-high neutrophil subset (Neu_CCL3) is significantly enriched in the pretreatment tumor microenvironment of patients who respond to nCIT.

  pretreatment microarray cohorts moc1 single-cell bulk immunohistochemistry

• 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 · 8 claims · 6 setups

  Has reproduction · 50

  IL-21-producing Tfh CD4 T cells repopulate after CD4 depletion but remain at reduced frequency compared with control mice

  cd44+ splenocytes spleen tcr scrna-seq flow spatial

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat