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).

• scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.

  PMID 42085187 · PMC13157062 · STAR protocols · 2026 · 8 claims · 6 setups

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  scPASU is a Snakemake-based workflow that quantifies APA from standard 3′ scRNA-seq data without requiring specialized library preparation

  ureter processed scrna-seq read poly

• A novel missense mutation in DAX-1 with an unusual presentation of X-linked adrenal hypoplasia congenita.

  PMID 17308433 · PMC3479083 · Hormone research · 2007 · 7 claims · 6 setups

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  A novel C794G transversion causing missense mutation T265R in DAX1 (NR0B1) is responsible for X-linked adrenal hypoplasia congenita in this kindred

  genomic tsa201 unspecified proband sequence modified full-length

• Evaluating imputation methods for accurate estimation of cell population fractions in single-cell RNA sequencing.

  PMID 41503159 · PMC12770975 · NAR genomics and bioinformatics · 2026 · 8 claims · 6 setups

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  Eight prominent imputation methods (MAGIC, SAVER, scVI, DCA, scBiG, kNN-smoothing, scImpute, ALRA) were systematically evaluated for their ability to recover the true non-zero expression fraction using simulated and real-world scRNA-seq data

  basal tracheal airway k562 simulated scrna-seq imputation

• 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

• 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

• 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

• PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

  PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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  PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

  pah scrna-seq pah-former candidate scrna-seq transfer perturbation

• Uropathogenic Escherichia coli invade luminal prostate cells via FimH-PPAP receptor binding.

  PMID 41507584 · PMC12872464 · Nature microbiology · 2026 · 8 claims · 8 setups

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  A 2D mouse stem cell-derived prostate epithelial organoid model was developed that mimics epithelial heterogeneity of the murine prostate

  prostate bladder immunofluorescence single-cell transepithelial

• Mosaic partial epidermal reprogramming remodels neighbors and niches to refine skin homeostasis and repair.

  PMID 41617708 · PMC12960685 · Nature communications · 2026 · 8 claims · 8 setups

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  A genetically engineered mouse model (Krt14-CreER; LSL-rtTA-EGFP; TetO-OSKM-mCherry, 'Epi-iOSKM') enables transient, reversible, mosaic OSKM expression in interfollicular epidermal cells without inducing pluripotency or teratoma risk

  epidermis sorted epidermal ife immunostaining single-cell pseudotime

• INTERFEROME: the database of interferon regulated genes.

  PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

  chimp ifn-treated tissues irg microarray in-house basal

• Utilization of genomic signatures to identify phenotype-specific drugs.

  PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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  A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

  nci-60 breast mda-mb-231 signature-drug gene signature

• Validation of bronchial airway gene expression associated with bronchiectasis in nasal epithelium.

  PMID 42094231 · PMC13139922 · ERJ open research · 2026 · 7 claims · 6 setups

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  No genes were significantly differentially expressed in nasal epithelium between participants with and without widespread radiologic BE (FDR<0.1)

  nasal bronchial bulk gene cell-type

• FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

  PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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  FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

  prostate targeted single-nucleus scatac-seq

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 4 setups

  Has reproduction · 87

  CoINcIDE is a novel framework for discovering patient subtypes across multiple datasets that requires no between-dataset transformations (e.g., batch correction)

  breast ovarian simulated gene consensus simulated

• TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.

  PMID 40124621 · PMC11929507 · PeerJ · 2025 · 8 claims · 8 setups

  Has reproduction · 79

  TGF-β signaling pathway activity is significantly increased in fibroblasts from cervical cancer samples compared to normal samples and correlates with tumor proliferation and differentiation.

  cervical tcga-cesc hela scrna-seq scrna-seq wgcna cox

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

  PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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  R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

  bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation

• Multi-modal skin atlas identifies a multicellular immune-stromal community associated with disrupted cornification and specific T cell expansion in atopic dermatitis.

  PMID 41741455 · PMC13057205 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a multi-modal single-cell atlas of 280,518 cells from 27 samples/17 adults (healthy, AD non-lesional/lesional, scleroderma), integrated with 430,186 cells from four prior studies into a 710,704-cell human skin atlas with 86 annotated granular cell subsets.

  skin healthy keratinocytes re-annotated droplet-based scrna-seq bulk

• Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

  PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

  Has reproduction · 66

  A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons

  fmr1-adarcd-v5 single bioinformatic drosophila immunofluorescence western bulk

• Small molecule inhibition rescues the skeletal dysplasia phenotype of Trpv4 mutant mice.

  PMID 41574606 · PMC12892883 · JCI insight · 2026 · 8 claims · 8 setups

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  Chondrocyte-specific (Col2a1-Cre-driven) expression of the p.R594H Trpv4 mutation reproduces the human TRPV4 skeletal dysplasia phenotype in mice, including short stature, long bone and craniofacial abnormalities, and vertebral defects.

  col2a1-cre proximal growth cervical radiography histology rnascope