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).

• Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments.

  PMID 18765474 · PMC2577354 · Nucleic acids research · 2008 · 6 claims · 6 setups

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  Extensive sonication reduces crosslinked chromatin to an average fragment size of ~200 bp (range 75–300 bp) and fragmentation is largely random with respect to genomic region and nucleosome position.

  cerevisiae hela chip-qpcr nucleosome gel

• Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

  PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

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  A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

  carcinoma derivative xenograft custom quantitative

• A hybrid empirical and parametric approach for managing ecosystem complexity: Water quality in Lake Geneva under nonstationary futures.

  PMID 35733249 · PMC9245694 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 7 claims · 6 setups

  Has reproduction · 69

  A hybrid model combining empirical dynamic modeling (EDM/S-map) for biogeochemical sink terms with the equation-based Simstrat hydrodynamic model for physical source terms produces substantially better historical DOB forecasts than conventional parametric models.

  lake convergent multivariate s-map

• Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens.

  PMID 34438997 · PMC8388888 · Antibiotics (Basel, Switzerland) · 2021 · 8 claims · 5 setups

  Has reproduction · 49

  The S. ambofaciens ATCC 23877 transcriptome was redefined from RNAseq data into 5587 transcriptional units (4433 monocistronic, 1154 polycistronic) covering 90.8% of the linear chromosome

  streptomyces ambofaciens bulk rna-seq target

• Genetic requirement for pneumococcal ear infection.

  PMID 18670623 · PMC2593789 · PloS one · 2007 · 7 claims · 8 setups

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  STM screening of 5,280 S. pneumoniae ST556 mutants in a chinchilla middle ear infection model identified 169 genes required for ear infection

  pneumoniae bioluminescent balb signature-tagged bioluminescent transmission

• DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

  PMID 17576693 · PMC1934997 · Nucleic acids research · 2007 · 6 claims · 7 setups

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  DNA bar coding combined with pyrosequencing allows parallel, deep characterization of drug resistance mutations across many HIV populations in a single experiment

  hiv pooled plasma pyrosequencing conventional rt-pcr

• Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons.

  PMID 18448472 · PMC2425497 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  Internal oligonucleotide calibration improves homozygote genotyping accuracy for base-pair neutral small amplicons from 91.7% to 99.7% across five of six targets

  genomic high-resolution sanger probe-based

• In vivo application of RNA interference: from functional genomics to therapeutics.

  PMID 16096010 · PMC7112075 · Advances in genetics · 2005 · 7 claims · 7 setups

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  RNAi operates through two mechanistically related but distinct pathways: cytoplasmic delivery of siRNA duplexes and nuclear delivery of shRNA expression cassettes that mimic miRNA

  mice tumor laser-induced herpetic cationic intraperitoneal aqueous

• Advanced Methods for Analyzing in-Situ Observations of Magnetic Reconnection.

  PMID 39234211 · PMC11369046 · Space science reviews · 2024 · 7 claims · 8 setups

  Has reproduction

  Collisionless magnetic reconnection in geospace has multi-scale structure: MHD regions (ions and electrons frozen-in), ion diffusion regions (ions demagnetized, electrons magnetized), and electron diffusion regions (both demagnetized, magnetic topology changes).

  solar multi-mission single mms maximum global mining

• Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.

  PMID 41345108 · PMC12789597 · Nature communications · 2025 · 7 claims · 8 setups

  Has reproduction · 93

  SIRT6 is an evolutionarily conserved regulator of tryptophan catabolism that balances tryptophan usage between the kynurenine and serotonin/melatonin pathways

  embryonic brains sirt6 serum untargeted rna-seq microarray

• Novel selection and genetic characterisation of an etoposide-resistant human leukaemic CCRF-CEM cell line.

  PMID 8382508 · PMC1968246 · British journal of cancer · 1993 · 8 claims · 5 setups

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  CEM/VP-1 is 15-fold more resistant to etoposide than parental CCRF-CEM cells

  ccrf-cem cem nuclear cytogenetic pcr allele-specific

• Application of proteomics in the study of tumor metastasis.

  PMID 15862116 · PMC5172469 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 8 setups

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  Cell function is directly regulated through proteins, not genes or mRNA, so metastasis-related gene findings need protein-level validation via proteomics.

  young metastatic hepatocellular lines microarray 2de cdna

• Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

  PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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  At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

  breast same selected hct116 expression methylation-specific rt-pcr

• Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

  PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 6 setups

  Has reproduction · 79

  CLSM6A, a CNN-based model set, predicts single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

  clsm6a learned last-layer computational model-based propagation-based