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).

• Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

  PMID 41490125 · PMC12768360 · PloS one · 2026 · 7 claims · 7 setups

  Has reproduction · 69

  Manual curation of RNA-seq-derived de novo transcripts increased the number of functional genes in the NWR annotation by 81% (from 8,701 to 15,738).

  southern granulosa nwr novo bulk isolation read

• Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

  PMID 20044523 · PMC2923092 · Stroke · 2010 · 8 claims · 6 setups

  Full-text index only

  SNP rs2208454 in intron 3 of MACROD2 (near FLRT3, chr20p12) is associated with lower risk of covert MRI-infarcts (OR=0.76, p=4.64x10-7)

  stroke-free elderly african-american cardiovascular genome-wide direct expression

• A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

  PMID 30833571 · PMC6399342 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 90

  16 genome-wide significant susceptibility loci for CTS were identified in UK Biobank

  biobank surgically gtex height gwas bulk summary

• Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

  PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

  Has reproduction · 79

  The 196 R. leguminosarum sv. trifolii strains constitute a five-species complex (genospecies gsA-gsE) that occur in sympatry but show little recent between-species gene transfer in core or accessory genomes, except for a few highly mobile regions.

  rhizobium leguminosarum strains orthologous whole-genome long-read 16s

• A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans.

  PMID 40629379 · PMC12239316 · BMC biology · 2025 · 8 claims · 7 setups

  Has reproduction · 54

  A 14-bp deletion in the KIT gene promoter region is associated with the all-white phenotype in yaks, identified via GWAS

  domestic re-sampled hek293t yak whole-genome pcr dual-luciferase

• Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.

  PMID 35922433 · PMC9349177 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction

  Genome-wide association of six CMR-derived aortic traits in up to 32,590 UK Biobank participants identifies 102 loci (including 27 novel associations) for aortic distensibility and area.

  biobank arterial aortic genome-wide multi-trait cardiac

• Structure of the intergenic spacers in chicken ribosomal DNA.

  PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups

  Has reproduction · 80

  Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.

  wag137g04 pacbio gallus_gallus-5.0 chicken long-read novo comparative

• A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis.

  PMID 18667089 · PMC2533022 · BMC genomics · 2008 · 7 claims · 2 setups

  Full-text index only

  HFCC is a method/software for genome-wide epistasis detection using case-control multi-locus association analysis, combining a fast computing algorithm with flexibility to test a variety of epistatic models.

  blood-derived simulated genome-wide simulation-based

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

  Full-text index only

  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• Genome-wide association studies in neurological disorders.

  PMID 18940696 · PMC2824165 · The Lancet. Neurology · 2008 · 8 claims · 6 setups

  Full-text index only

  GWAS can identify common genetic variability associated with a trait across the whole genome, avoiding the bias and low throughput of candidate-gene studies

  icelandic german north sclerosis genome-wide multistage

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

  saanen goat testicular saanen_v1 pacbio illumina hi-c

• Analysis of genetic variability and whole genome linkage of whole-brain, subcortical, and ependymal hyperintense white matter volume.

  PMID 19834011 · PMC2787844 · Stroke · 2009 · 8 claims · 5 setups

  Full-text index only

  Whole-brain, subcortical, and ependymal HWM volumes are all highly heritable

  mexican extracted same structural genotyping heritability

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr

• RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

  PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 41

  Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

  pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

• The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.

  PMID 41131451 · PMC12551222 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 8 setups

  Has reproduction

  Significant genetic introgression from Chinese pigs into commercial European lines was confirmed, with introgressed segments predominantly deriving from Southern Chinese domestic pigs (CSDP) with additional contributions from Eastern Chinese domestic pigs (CEDP).

  pigs duroc muscle snp whole-genome low-coverage

• Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

  PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

  longissimus muscle snps pig h3k27ac strand-specific starr-seq

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript