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).

• Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

  PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

  inhbb cloned same fresh-frozen rnase masscleave clonal

• 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

• Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

  PMID 36253367 · PMC9576764 · Nature communications · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  The P. magna mitoribosome contains rRNA split into 13 fragments (LSU1-8, SSU1-4, mt-5S)

  mitoribosome polytomella cross-species single-particle novo comparative

• A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

  PMID 19828875 · PMC2816009 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 6 setups

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  A stacked-ring ion guide (S-lens) increases ion transmission from the source into the instrument roughly 10-fold in MS/MS mode and 3-5-fold in full scan mode

  intact bsa hela model top-down nanoflow ion

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

  PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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  An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

  acid-extracted hela online offline

• Proteomic analysis of mechanisms of hypoxia-induced apoptosis in trophoblastic cells.

  PMID 17299580 · PMC1796955 · International journal of medical sciences · 2006 · 8 claims · 7 setups

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  Hypoxia induces apoptosis in JAR trophoblastic cells, shown by time-dependent increase in internucleosomal DNA fragmentation

  jar powerblot mtt death

• A comparison of programmed cell death between species.

  PMID 11178240 · PMC138857 · Genome biology · 2000 · 8 claims · 8 setups

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  The core apoptotic pathway (CED-3/caspases, CED-4/Apaf-1, CED-9/Bcl-2, EGL-1) is conserved across C. elegans, Drosophila, and mammals.

  elegans mammalian drosophila transgenic whole-genome kinetic ectopic

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr

• Decision tree-driven tandem mass spectrometry for shotgun proteomics.

  PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups

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  A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone

  saccharomyces proteome embryonic nlc-ms phosphoproteomics sequential

• Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

  PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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  PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

  porcine paec umbilical huvec methyltransferase sds-page fragmentation

• Global mapping of the topography and magnitude of proteolytic events in apoptosis.

  PMID 18724940 · PMC2597167 · Cell · 2008 · 7 claims · 6 setups

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  PROTOMAP, a method combining 1D SDS-PAGE fractionation with LC-MS/MS-derived sequence coverage and spectral counting visualized as 'peptographs', enables global mapping of proteolytic topography and magnitude

  jurkat sds-page fragmentation caspase-3

• Targeted KRAS mutation assessment on patient tumor histologic material in real time diagnostics.

  PMID 19888477 · PMC2768905 · PloS one · 2009 · 8 claims · 5 setups

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  Q-PCR methods yield informative KRAS mutation results even on very fragmented FFPE-DNA where dideoxy-sequencing fails (p<0.0001)

  ffpe dideoxy-sequencing taqman-mgb dxs-kras

• What's Genetic Variation Got to Do with It? Starvation-Induced Self-Fertilization Enhances Survival in Paramecium.

  PMID 32163147 · PMC7239694 · Genome biology and evolution · 2020 · 8 claims · 5 setups

  Has reproduction · 89

  Self-fertilization enhances heat shock resistance in P. tetraurelia in the absence of new genetic variation

  paramecium heat autogamy bulk

• Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.

  PMID 36513983 · PMC9749362 · BMC bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 99

  Long-read classifiers generally performed best among the 11 methods tested

  atcc zymobiomics taxonomic short-read

• transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.

  PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups

  Has reproduction · 95

  transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms

  piper assembled longum predicted rna-seq novo transcriptome

• Mining the draft human genome.

  PMID 11236999 · PMC2658632 · Nature · 2001 · 8 claims · 7 setups

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  Protein-coding exons account for only about 3% of the human genome DNA, with repeat sequences making up around 46%.

  genome unfinished drosophila tetraodon psi-blast domain sequence

• A rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and ELISA microarrays.

  PMID 15502246 · PMC3839270 · Disease markers · 2004 · 8 claims · 4 setups

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  A two-stage strategy combining MS proteomics for discovery and ELISA microarrays for validation can identify and characterize cancer markers in very small samples

  complex naf minute clc-fticr tandem elisa

• High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy.

  PMID 17184556 · PMC1797031 · Breast cancer research : BCR · 2006 · 8 claims · 8 setups

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  Plasma is well suited to proteomic biomarker discovery because it is easily obtained, routinely used diagnostically, and has a rich proteome.

  plasma serum maldi-tof seldi-tof tandem

• Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

  PMID 18157127 · PMC2397541 · Nature genetics · 2008 · 8 claims · 8 setups

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  Homozygous truncating mutations in PCNT cause Seckel syndrome

  consanguineous genomic lymphoblastoid lcls snp-microarray sanger immunofluorescence