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).

• Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

  PMID 20041192 · PMC2793532 · PloS one · 2009 · 7 claims · 5 setups

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  Quantitative proteomics of conditioned medium from BACE1-overexpressing HEK and HeLa cells identified 68 putative β-secretase substrates

  hek293 hela hek concentrated silac western sds-page

• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

  PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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  Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

  gingivalis whole-cell comparative gene

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• Relation of response to treatment with dorzolamide in X-linked retinoschisis to the mechanism of functional loss in retinoschisin.

  PMID 18834580 · PMC2668603 · American journal of ophthalmology · 2009 · 6 claims · 4 setups

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  A positive response of macular cysts to dorzolamide can occur across all three known mechanisms of retinoschisin dysfunction (absent secretion, decreased expression, non-functional secretion).

  eyes blood-derived ebna xlrs optical genetic transfection

• 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

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

  PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  LTR8B is a placentally-relevant cis-regulatory element (CRE), notably within the PSG array

  sghpl-4 bewo recombinant serum chip-exonuclease transient quantitative