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).

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 99

  Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.

  coli lymphoblastoid na12878 mixture nanopore cas9-targeted whole-genome

• Back to basics.

  PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

  chromosome pendrin yeast carbonic genome gene mudpit

• "Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

  PMID 18973698 · PMC2583995 · Journal of translational medicine · 2008 · 7 claims · 6 setups

  Full-text index only

  An oligo-array platform can detect BRCA1 SNPs, insertions, and deletions of known and unknown variants, including in heterozygous conditions, with accuracy comparable to direct sequencing

  genomic pcr mcf-10a brca1 oligo-nucleotide direct pcr

• Biodefense versus bioterrorism.

  PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups

  Full-text index only

  Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask

  bacillus ancestral cultures anthrax whole-genome comparative colony

• DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

  PMID 18628296 · PMC2504308 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  Digital PCR compartmentalizes individual bisulfite-converted DNA template molecules into separate wells, enabling single-molecule DNA methylation analysis

  fresh-frozen same sssi-methylated mixture digital conventional classic

• Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX.

  PMID 19864251 · PMC2811011 · Nucleic acids research · 2010 · 7 claims · 8 setups

  Full-text index only

  SPEX-type approaches preferentially access genetic information from damaged, degraded endogenous ancient DNA templates over modern human contaminant DNA

  iceman hb50 pe168 lq4 relative pcr spex

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Cell fixation and preservation for droplet-based single-cell transcriptomics.

  PMID 28526029 · PMC5438562 · BMC biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  Methanol fixation stabilizes and preserves dissociated cells for weeks without compromising single-cell RNA-seq data quality

  hek293 dissociated facs-sorted hek drop-seq bulk trizol

• A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

  PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

  Full-text index only

  Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

  falciparum cloned pyrosequencing pcr

• Minisequencing mitochondrial DNA pathogenic mutations.

  PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

  Full-text index only

  A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

  blood-derived same genomic pcr minisequencing automatic multiplex

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe.

  PMID 16432256 · PMC1345699 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  A 17mer PNA spanning K-ras codons 12/13 can serve as both PCR clamp and sensor probe in a single-tube reaction, differentiating all 12 possible point mutations from wild-type by melting temperature shift

  wild-type mixture mutant serial melting real-time limit-of-detection

• Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

  PMID 16404425 · PMC2361188 · British journal of cancer · 2006 · 7 claims · 8 setups

  Full-text index only

  A G274A base substitution in hnRNP K mRNA is present in colorectal tumours and surrounding mucosa but absent from corresponding genomic DNA, indicating an RNA editing event rather than a germline polymorphism.

  colorectal cdna matched thyroid rt-pcr restriction genomic

• Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

  PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

  Full-text index only

  HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

  plasma proviral cloned pbmc hiv-1 nested clonal

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

  Full-text index only

  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal