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).

• Microglia maintain structural integrity during fetal brain morphogenesis.

  PMID 38309258 · PMC10869139 · Cell · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  Embryonic ATM-like microglia accumulate at two fetal cortical boundaries, the cortico-striato-amygdalar boundary (CSA) and cortico-septal boundary (CSB), resembling post-natal axon-tract-associated microglia (ATM)

  embryonic cx3cr1 fetal embryos single-cell immunolabeling phrodo

• Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

  PMID 32542016 · PMC7295234 · PloS one · 2020 · 7 claims · 8 setups

  Has reproduction · 51

  Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC compared to normal liver at mRNA and/or protein level

  oncomine tcga-lihc gse89377 hcc pan-cancer bulk microarray

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 7 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm via an evolutionarily conserved intronic enhancer

  e9.5 xenopus bulk rt-qpcr whole-mount

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells represent largely distinct, non-overlapping populations across murine and human aging tissues

  hippocampus brain skeletal bone scrna-seq cytof velocity

• 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

• Application of Machine Learning in Predicting Hepatic Metastasis or Primary Site in Gastroenteropancreatic Neuroendocrine Tumors.

  PMID 37887568 · PMC10605255 · Current oncology (Toronto, Ont.) · 2023 · 8 claims · 7 setups

  Has reproduction · 59

  Multi-gene random forest models classify primary tumor vs. liver metastasis samples with 100% accuracy in training/test cohorts and >90% accuracy in an independent validation cohort

  pancreatic rna-seq liver tumor bulk machine multi-label

• Comprehensive comparison of gene expression diversity among a variety of human stem cells.

  PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 71

  Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types

  escs stem batch-corrected degs bulk batch dimensionality

• Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

  PMID 34719737 · PMC8629906 · Cellular and molecular life sciences : CMLS · 2021 · 7 claims · 8 setups

  Has reproduction · 50

  VAP-1 is expressed on a subset of human HSC and on bone marrow vasculature forming a hematogenic niche

  bone sorted cord femur flow bulk single-cell

• Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.

  PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups

  Has reproduction · 23

  COPD GWAS risk loci are statistically more clustered across the genome than expected by chance, with chromosome 4q containing a notably dense cluster of five loci within 70Mb.

  lung genes independent genome-wide rna-seq partial gene

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.

  PMID 35922433 · PMC9349177 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction

  Genome-wide association of six CMR-derived aortic traits in up to 32,590 UK Biobank participants identifies 102 loci (including 27 novel associations) for aortic distensibility and area.

  biobank arterial aortic genome-wide multi-trait cardiac

• Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

  PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

  adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics

• HIV-1 Nef binds the DOCK2-ELMO1 complex to activate rac and inhibit lymphocyte chemotaxis.

  PMID 14737186 · PMC314466 · PLoS biology · 2004 · 8 claims · 8 setups

  Full-text index only

  HIV-1 Nef binds the DOCK2-ELMO1 complex (which also contains Rac) in T cells

  jurkat hek resting ns1 two-step ni-nta anti-flag

• Genome-wide microRNA profiling in human fetal nervous tissues by oligonucleotide microarray.

  PMID 16983573 · PMC1705512 · Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2006 · 8 claims · 5 setups

  Full-text index only

  72-83% of assayed miRNAs are expressed across human fetal organs, with G24w cerebrum showing the most miRNAs expressed

  fetal same microarray oligonucleotide northern microarray

• A novel POMT2 mutation causes mild congenital muscular dystrophy with normal brain MRI.

  PMID 18804929 · PMC2702532 · Brain & development · 2009 · 6 claims · 8 setups

  Full-text index only

  A novel homozygous POMT2 mutation (c.604T>G, p.F202V) causes mild congenital muscular dystrophy with normal brain MRI

  skeletal genomic cos serum immunohistochemistry immunoblotting laminin

• In silico discovery of transcription regulatory elements in Plasmodium falciparum.

  PMID 18257930 · PMC2268928 · BMC genomics · 2008 · 7 claims · 8 setups

  Full-text index only

  GEMS, using hypergeometric scoring and PWM parameter optimization, reliably identifies high-confidence cis-regulatory elements in the AT-rich, repeat-rich P. falciparum genome

  falciparum plasmodium invasion invasion-related microarray motif comparative

• A novel recessive Nefl mutation causes a severe, early-onset axonal neuropathy.

  PMID 20039262 · PMC4439312 · Annals of neurology · 2009 · 8 claims · 8 setups

  Full-text index only

  A homozygous NEFL nonsense mutation (E210X) causes a severe, early-onset recessive axonal neuropathy in four siblings of a consanguineous family

  family sural nefl-null sw-13 clinical genetic immunohistochemistry

• A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

  PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups

  Full-text index only

  Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)

  genomic hek293 hepg2 microsomes pcr site-directed luciferase

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

  Full-text index only

  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based