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).

• Kinetoplastid genomics: the thin end of the wedge.

  PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

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  Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

  brucei major cruzi kinetoplastid whole-genome gene shotgun

• Human QTL linkage mapping.

  PMID 18668207 · PMC2761031 · Genetica · 2009 · 8 claims · 6 setups

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  Human QTL linkage mapping remains a productive approach for complex traits despite the perception that it does not work, and will continue to be productive especially combined with RNA expression QTLs and dense SNP panels

  mexican pomc gene promoter genome-wide gene expression

• A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.

  PMID 18628483 · PMC2561321 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 6 claims · 7 setups

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  A novel heterozygous BRIP1 germline mutation (c.2992-2995delAAGA) was identified in a breast cancer patient, causing a frameshift and premature stop codon in exon 20.

  genomic laser-capture cell-free hela sscp loss transcription

• The genomic analysis of erythrocyte microRNA expression in sickle cell diseases.

  PMID 18523662 · PMC2408759 · PloS one · 2008 · 8 claims · 8 setups

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  Mature human erythrocytes lack ribosomal/large RNAs but contain abundant and diverse microRNAs

  mature erythrocytes k562 erythrocyte microrna size northern

• Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

  PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

  cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

• Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

  PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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  Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

  families genes individuals kidney genome-wide sanger resequencing

• A small-cell lung cancer genome with complex signatures of tobacco exposure.

  PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

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  22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

  nci-h209 sclc lu-135 massively pcr multiplex

• A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

  PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

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  The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

  aureus 2-d 1-d gelc-ms

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

  PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

  sporadic wilms fetal 293t loh multiplex genome-wide

• Nitrosative stress-induced s-glutathionylation of protein disulfide isomerase leads to activation of the unfolded protein response.

  PMID 19773442 · PMC2756322 · Cancer research · 2009 · 7 claims · 8 setups

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  PABA/NO treatment causes S-glutathionylation (not S-nitrosylation) of PDI in cells and in vitro

  skov3 recombinant mtt daf-fm-da immunoprecipitation

• A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

  PMID 19728872 · PMC2745377 · BMC medical genetics · 2009 · 8 claims · 7 setups

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  A novel homozygous missense mutation, c.1922G>A (p.Arg641His), in MANBA was identified in a patient with severe neurological disease featuring pyramidal and cerebellar involvement, a phenotype not previously reported in β-mannosidosis.

  family hek293t lymphoid pcr-amplified fluorometric site-directed western

• Recurring mutations found by sequencing an acute myeloid leukemia genome.

  PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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  Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

  aml-m1 tumor bone additional whole-genome snp gene-expression

• Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.

  PMID 39018396 · PMC466953 · Science advances · 2024 · 8 claims · 8 setups

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  Primate-specific ERVs are a rich source of enhancers displaying cancer-specific activity across multiple tumor types

  cancer hct116 tcga colorectal atac-seq chip-seq bulk

• Systems biology of gene regulation fulfills its promise.

  PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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  Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

  unspecified embryonic five yeast chip-chip chip-pet computational

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• ENCODE whole-genome data in the UCSC Genome Browser.

  PMID 19920125 · PMC2808953 · Nucleic acids research · 2010 · 7 claims · 8 setups

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  The UCSC ENCODE Data Coordination Center serves as the primary repository for ENCODE experimental results, providing access via Genome Browser, Table Browser, and FTP download.

  lines chip-seq dnase-seq rna-seq