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).

• The rate of the 6174delT founder Jewish mutation in BRCA2 in patients with non-colonic gastrointestinal tract tumours in Israel.

  PMID 11207041 · PMC2363777 · British journal of cancer · 2001 · 8 claims · 2 setups

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  The 6174delT BRCA2 mutation carrier rate is significantly higher in Jewish Ashkenazi non-colonic GI cancer patients (8.6%) than in the general Ashkenazi population (1.16%)

  unselected peripheral extraction pcr

• CoMoDis: composite motif discovery in mammalian genomes.

  PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

  ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored

• TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

  PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups

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  Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)

  ovarian sporadic paraffin-embedded mutation survival extraction

• Prevalence of von Hippel-Lindau gene mutations in sporadic renal cell carcinoma: results from The Netherlands cohort study.

  PMID 15932632 · PMC1177929 · BMC cancer · 2005 · 7 claims · 4 setups

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  VHL mutations were detected in 61% (114/187) of sporadic clear-cell RCC patients

  archival subset flanking paraffin-embedded pcr-sscp feasibility histopathological

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Fucosylated glycoproteins as markers of liver disease.

  PMID 19126969 · PMC3827789 · Disease markers · 2008 · 8 claims · 6 setups

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  Core alpha 1,6-linked fucosylation of AFP (AFP-L3) is increased in HCC and is a more specific marker of HCC than total AFP

  afp pooled larger igg lectin fucose-specific immunoblot

• Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

  PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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  Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

  deposit excised pooled worn sds-page in-gel lc-ms-ms

• Microproteomics: analysis of protein diversity in small samples.

  PMID 18271009 · PMC2743962 · Mass spectrometry reviews · 2008 · 8 claims · 8 setups

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  Changes in gene/mRNA expression often do not correlate well with changes in protein expression, due to precursor cleavage, post-translational modification, localization, and variable protein lifetimes.

  lcm-dissected single few dense gel maldi capillary

• Proteomic analysis of RCL2 paraffin-embedded tissues.

  PMID 19012729 · PMC4506168 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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  RCL2-fixed paraffin-embedded (RCL2P) tissue consistently gives the highest protein yield compared to FFPE and frozen tissue across extraction protocols

  normal rcl2p ffpe frozen yield 1-dimensional 2-dimensional

• Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

  PMID 18974839 · PMC2572839 · PloS one · 2008 · 7 claims · 6 setups

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  Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients

  ileal p16s otu pseudomonas nested cloning

• Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.

  PMID 18984079 · PMC2679897 · American journal of obstetrics and gynecology · 2008 · 8 claims · 7 setups

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  Women with severe preeclampsia present a unique urinary proteomic fingerprint distinguishable from controls.

  urine placenta placental seldi-tof tandem spiking

• Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.

  PMID 35177610 · PMC8854666 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  SHARC uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA

  model dipicolinic hek293t 28s crosslinking nmr crosslink