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).

• Comparative proteomics of clathrin-coated vesicles.

  PMID 17116749 · PMC2064594 · The Journal of cell biology · 2006 · 8 claims · 4 setups

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  A comparative proteomics strategy contrasting CCV fractions from control and clathrin-depleted (CHC siRNA knockdown) HeLa cells can distinguish genuine CCV proteins from copurifying contaminants

  hela western sds-page difference

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

• Harnessing the HGP of public health.

  PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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  The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

  carnation cirv blood rice x-ray site-directed mass

• Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

  PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups

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  The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes

  schistosoma brugia ancylostoma echinococcus whole-genome interference transgenesis

• A computational study of off-target effects of RNA interference.

  PMID 15800213 · PMC1072799 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  The chance of RNAi off-target effects is considerable, ranging from 5% to 80% depending on organism and parameters, when using exact sequence identity between siRNA and transcripts.

  schizosaccharomyces caenorhabditis homo pombe off-target mismatch-tolerant rational

• Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

  PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls

  activated skeletal muscle altered affymetrix quantitative sirna

• Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

  PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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  APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

  magi pbmc 293t supt1 sensitive rt-pcr western

• A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

  PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

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  FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

  chimpanzee hepg2 promoters liver quantitative western sirna

• Metabolomics applied to diabetes research: moving from information to knowledge.

  PMID 19875619 · PMC2768174 · Diabetes · 2009 · 8 claims · 7 setups

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  Metabolomics measures chemical phenotypes that are the net result of genomic, transcriptomic, and proteomic variability, providing the most integrated profile of biological status

  ins-1-derived pancreatic liver stedman 13c targeted ms-based

• Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

  PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

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  Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

  gria2 drosophila nova1 cd45 splicing sirna hits-clip

• Enhanced IFNy response in dedifferentiated melanoma cells is due to chromatin remodeling as revealed by ATAC-seq.

  PMID 41904529 · PMC13217986 · Cell communication and signaling : CCS · 2026 · 8 claims · 7 setups

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  MITF knockdown and IFNγ stimulation each produce substantial but distinct changes in chromatin accessibility in 624Mel melanoma cells

  624mel melanoma atac-seq western motif

• PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells.

  PMID 41694110 · PMC12902810 · Experimental and therapeutic medicine · 2026 · 7 claims · 7 setups

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  PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells

  h9c2 rt-qpcr western counting

• LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis.

  PMID 41735607 · PMC12992122 · Nature cell biology · 2026 · 7 claims · 8 setups

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  Combined downregulation of 12 abundant, ubiquitously expressed nuclear envelope proteins (si-11) causes global detachment of constitutive heterochromatin from the nuclear envelope and its relocation to the nuclear interior in multiple mammalian cell types

  hct116 rpe-1 nih immunofluorescence immunoblot sequencing

• A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 8 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22

  atlas roadmap liver-specific kidney co-expression transcription reanalysis

• Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

  PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups

  Has reproduction · 96

  ID-seq combines DNA-tagged antibodies with high-throughput sequencing to enable large-scale, high-dimensional, multiplexed (phospho-)protein phenotyping in fixed cell populations across many samples in parallel.

  epidermal id-seq immuno-pcr colony

• Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.

  PMID 32959884 · PMC7689298 · Human molecular genetics · 2020 · 8 claims · 8 setups

  Has reproduction · 67

  Trem2 R47H knock-in mice show gene dose-dependent decreased Trem2 expression in hippocampus, largely due to altered splicing

  hippocampal microglia conditioned rt-qpcr immunohistochemistry glial

• Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling.

  PMID 29187638 · PMC5721160 · Journal of the Royal Society, Interface · 2017 · 8 claims · 8 setups

  Has reproduction · 49

  Numb/Numbl acts as a 'phenotypic stability factor' (PSF) that inhibits a complete EMT by stabilizing the hybrid E/M phenotype

  single-cell lattice h1975 ode-based multi-cell sirna

• TGF-β-dependent reprogramming of amino acid metabolism induces epithelial-mesenchymal transition in non-small cell lung cancers.

  PMID 34168290 · PMC8225889 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  TGF-β induces reprogramming of intracellular amino acid metabolism that is necessary to promote EMT in NSCLC cells

  a549 metabolomics real-time western

• Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma.

  PMID 33420019 · PMC7794422 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 50

  SNAI2 is highly expressed in FN-RMS tumors and cell lines compared to normal tissue

  rms fn-rms fp-rms imr90 rna-seq western immunohistochemistry

• FOXM1 inhibitor, RCM‑1, enhances venetoclax mediated apoptosis through downregulation of ATP2B4 in rhabdomyosarcoma.

  PMID 41789627 · PMC12987556 · International journal of oncology · 2026 · 8 claims · 8 setups

  Has reproduction · 10

  Combination therapy of RCM-1 and venetoclax inhibits RMS tumor growth more efficiently than venetoclax alone in an animal model by decreasing proliferation and inducing apoptosis

  rms injected muscle cck-8 caspase subcutaneous