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).

• Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

  PMID 17052347 · PMC1622754 · BMC infectious diseases · 2006 · 8 claims · 4 setups

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  TMA/IHC staining patterns of GroEL, GroES, GspD, Ndk and Pyk in cell pellets generally corresponded to differential regulation patterns previously found by 2D gel proteomic analysis of IFN-γ-induced persistence

  hep-2 archival pneumoniae immunohistochemistry western gel

• Genome-wide microRNA profiling in human fetal nervous tissues by oligonucleotide microarray.

  PMID 16983573 · PMC1705512 · Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2006 · 8 claims · 5 setups

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  72-83% of assayed miRNAs are expressed across human fetal organs, with G24w cerebrum showing the most miRNAs expressed

  fetal same microarray oligonucleotide northern microarray

• GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

  PMID 16919418 · PMC2842930 · Genomics · 2006 · 8 claims · 8 setups

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  Human FXN YAC transgenes containing GAA repeat expansions (YG22, YG8) rescue the embryonic lethality of homozygous Fxn knockout mice

  yg22 tissues lysates sciatic breeding semiquantitative western

• Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

  PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

  tissues inter-subspecies placenta genomic microarray rt-pcr sequencing

• MitoP2: the mitochondrial proteome database--now including mouse data.

  PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

  saccharomyces yeast heart liver genome-wide single transcriptome

• Organismal complexity, cell differentiation and gene expression: human over mouse.

  PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

  human-mouse oligonucleotide exon comparative

• Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

  PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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  Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

  placenta five lines huh7 5'-race rt-pcr real-time

• Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

  PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

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  KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

  embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin

• Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

  PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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  A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

  gbs clinical bioinformatic eburst kinetic

• Nicotinic acetylcholine receptor subunit variants are associated with blood pressure; findings in the Old Order Amish and replication in the Framingham Heart Study.

  PMID 18625075 · PMC2478679 · BMC medical genetics · 2008 · 7 claims · 5 setups

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  A synonymous coding SNP (rs2099489) in CHRNG is associated with higher systolic blood pressure in both the Old Order Amish (AFDS) and the Framingham Heart Study

  amish non-first-degree-relative afds framingham variance direct snp

• Atrial natriuretic peptide frameshift mutation in familial atrial fibrillation.

  PMID 18614783 · PMC2518320 · The New England journal of medicine · 2008 · 7 claims · 5 setups

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  A heterozygous frameshift mutation in NPPA (encoding atrial natriuretic peptide, ANP) causes familial atrial fibrillation

  family plasma atria genome-wide fine exon

• Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

  PMID 20006904 · PMC2814002 · Neuropeptides · 2010 · 8 claims · 5 setups

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  Bioinformatic survey of chicken genome/EST/HTGS databases identifies previously unreported chicken neuropeptide genes

  chicken blast microarray est

• A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

  PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

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  The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

  carp randomly zebrafish reciprocal sequence microarray

• Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

  PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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  Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

  apc-deficient heart ileum fresh-frozen spatial high-resolution bulk

• Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

  PMID 41821037 · PMC12983708 · Genome biology · 2026 · 8 claims · 8 setups

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  Horizontal integration of scRNA-seq and snRNA-seq improves cell-type identification

  renal kidney pbmc heart scrna-seq snrna-seq snatac-seq

• Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes.

  PMID 41526351 · PMC12796357 · Nature communications · 2026 · 8 claims · 8 setups

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  Cardiomyocyte (CM)-specific Hi-C data detect substantially more and stronger promoter-interacting domains (PIDs) for CM marker genes than bulk cardiac tissue Hi-C data

  non-failing cardiac nf-lv-cm biological hi-c fluorescence-activated chip-seq

• Genome Wide Association Studies: identifying the genes that determine the risk of abdominal aortic aneurysm.

  PMID 18621558 · PMC2697027 · European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery · 2008 · 8 claims · 3 setups

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  AAA has a strong genetic component, with up to ten-fold increased risk in first-degree relatives of affected individuals

  aaa cases candidate genome-wide

• Identification of novel homologous microRNA genes in the rhesus macaque genome.

  PMID 18186931 · PMC2254598 · BMC genomics · 2008 · 8 claims · 2 setups

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  454 rhesus miRNA genes were identified in total, including 383 novel genes in addition to 71 previously reported

  rhesus genome polya

• Harnessing the HGP of public health.

  PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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  The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

  carnation cirv blood rice x-ray site-directed mass

• International sequencing consortium.

  PMID 15174459 · PMC1315987 · Environmental health perspectives · 2004 · 8 claims · 6 setups

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  The p19 viral silencing-suppressor protein selectively recognizes short (21-22 nt) silencing siRNAs by measuring duplex length, using tryptophan residues (Trp39, Trp42) as molecular calipers that stack against the siRNA end base pairs.

  cirv blood sampled rice x-ray site-directed mass