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).
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Has reproduction · 87
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups
mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.
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Has reproduction · 70
The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease.
PMID 38839750 · PMC11153611 · Nature communications · 2024 · 8 claims · 8 setups
Intestinal epithelial cell-specific deletion of Slc39a8 causes systemic manganese (Mn) deficiency in blood and multiple organs.
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Has reproduction · 71
Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.
PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 7 claims · 7 setups
TCDD elicits dose-dependent AHR-mediated differential expression of hepatic lncRNAs in both mouse and rat liver, with more DE lncRNAs in mice than rats and a subset conserved across species.
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Biphasic expression of thyroid hormone receptor TRβ1 in mammalian retina and anterior ocular tissues.
PMID 37033230 · PMC10076699 · Frontiers in endocrinology · 2023 · 7 claims · 8 setups
TRβ1 shows a biphasic, late-peaking expression profile in retina that contrasts with the early embryonic peak of TRβ2
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Modeling chromosomes in mouse to explore the function of genes, genomic disorders, and chromosomal organization.
PMID 16839184 · PMC1500809 · PLoS genetics · 2006 · 8 claims · 8 setups
Cre/loxP recombination in ES cells can generate megabase-scale deletions, duplications, and inversions depending on loxP orientation, cis/trans configuration, and cell cycle stage
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Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.
PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups
CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.
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Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.
PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups
Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster
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Neuroscience in the era of functional genomics and systems biology.
PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups
Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.
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Has reproduction · 96
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.
PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups
An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.
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Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity
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Has reproduction · 73
Vespucci: a system for building annotated databases of nascent transcripts.
PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups
Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.
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Has reproduction · 75
Why an integrated view of gene expression studies on hematopoiesis in mouse aging is better than the sum of their parts.
PMID 38627103 · PMC11586588 · FEBS letters · 2024 · 7 claims · 4 setups
Combining differentially expressed (DE) gene lists from multiple publications into a unified 'aging list' (AL) with citation counts, and deriving a shorter high-confidence 'aging signature' (AS, genes cited in >3 publications, ~200 genes), produces a more reliable and consistent picture of hematopoietic aging than any single study.
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The oxazolidinone derivative locostatin induces cytokine appeasement.
PMID 19917702 · PMC2799496 · Journal of immunology (Baltimore, Md. : 1950) · 2009 · 7 claims · 7 setups
RKIP is differentially localized (not differentially expressed) on the proteomic map after in vivo T cell recall compared to resting state
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Understanding sex differences in environmental health: a thought leaders' roundtable.
PMID 15064168 · PMC1241928 · Environmental health perspectives · 2004 · 8 claims · 8 setups
Dioxin and corticosteroids both cause thymic atrophy but via distinct mechanisms; dioxin's atrophy kinetics resemble those induced by estrogen despite acting through a different receptor.
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Has reproduction · 67
The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.
PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups
A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.