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).

• Lamin C is required to establish genome organization after mitosis.

  PMID 34775987 · PMC8591896 · Genome biology · 2021 · 7 claims · 6 setups

  Has reproduction · 76

  Lamin C, and not lamin A or lamin B1, is required for LAD:LAD cohesion, retention of LADs near the nuclear envelope, and overall chromosome territory organization.

  embryonic mefs clonal western growth damid-seq

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

  Full-text index only

  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• Identification of new ETV6 modulators through a high-throughput functional screening.

  PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

  reh genome-wide qrt-pcr chip-seq

• Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.

  PMID 37810000 · PMC10559070 · Heliyon · 2023 · 7 claims · 7 setups

  Has reproduction · 88

  SEA and SEB treatment increases proliferation of AML cell lines.

  aml cancer proliferation cytotoxicity transwell

• Genetic and functional association of FAM5C with myocardial infarction.

  PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

  Full-text index only

  SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

  genecard cathgen donor aortic genome-wide case-control expression

• Systems biology in human health and disease.

  PMID 17893698 · PMC2013921 · Molecular systems biology · 2007 · 8 claims · 5 setups

  Full-text index only

  High-throughput quantitative proteomics of signaling networks (e.g., HER2 overexpression) can be correlated with biological responses like proliferation and migration to better understand pathways deregulated in cancer.

  her2 biological prostate model quantitative combinatorial genome-wide

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray

• AgBase: a functional genomics resource for agriculture.

  PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.

  pasteurella chicken maize gene proteogenomic mudpit differential

• Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.

  PMID 33634984 · PMC7882098 · Clinical and translational medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  JMJD6 is an epigenetic vulnerability/fitness gene in RCC, identified by integrating GeCK CRISPR screening data with TCGA/ICGC RCC cohorts.

  tumor rcc 786-o balb crispr mtt sirna

• Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

  PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation

  quiescent satellite regenerating situ atac-seq rna-seq motif

• Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.

  PMID 40721291 · PMC12305944 · Life science alliance · 2025 · 8 claims · 7 setups

  Has reproduction · 74

  Acute MYC (T58I) and BCL2 overexpression drives an aberrant B-cell differentiation phenotype with altered surface marker expression while functional antibody secretion is retained

  peripheral rna-seq flow edu antibody

• An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

  PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 88

  SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

  kidney tubuloids immunodeficient tub rt-qpcr western histology

• The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.

  PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se

  sez-derived computational nsc npc atac-seq bulk lisa

• Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

  PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

  Full-text index only

  Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

  mcf7 promoter cdna quantitative computational

• mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

  PMID 18980691 · PMC2612029 · BMC genomics · 2008 · 8 claims · 8 setups

  Full-text index only

  mtDNA depletion confers specific, shared gene expression profiles in A549 cells grown in culture and as xenografts

  a549 growth oxygen mtdna

• PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

  PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 7 claims · 8 setups

  Has reproduction · 76

  PI3K/mTOR/Akt inhibitors are a pharmacological class that represses glucocorticoid-induced REDD1 and FKBP51 expression, identified via LINCS drug-repurposing screen.

  transcriptome hacat c57bl transcriptional rt-pcr luciferase

• JunB Is Critical for Survival of T Helper Cells.

  PMID 35837408 · PMC9273772 · Frontiers in immunology · 2022 · 7 claims · 7 setups

  Has reproduction · 69

  JunB is required for clonal expansion of Th1, Th2, and Th17 cells

  ot-ii junb naive th1 flow adoptive th1