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).

• Sources of variability and effect of experimental approach on expression profiling data interpretation.

  PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

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  Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

  skeletal muscle spleen myogenic affymetrix duplicate unsupervised

• 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

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• GENCODE: producing a reference annotation for ENCODE.

  PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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  GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

  tissues encode rt-pcr comparative automated

• 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

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells represent largely distinct, non-overlapping populations across murine and human aging tissues

  hippocampus brain skeletal bone scrna-seq cytof velocity

• TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

  PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles

  fischer computational transcriptomic same bulk gan-based autoencoder

• Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

  PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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  A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

  bovine pcr-based comparative rt-pcr

• MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

  PMID 18154640 · PMC2233610 · BMC medical genetics · 2007 · 8 claims · 6 setups

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  Chromosome 8p23.1 has previously been proposed as a nuclear modifier locus for A1555G-associated hearing loss phenotype

  blood a1555g lymphoblastoid nuclear pcr-rflp direct rt-pcr

• Cold-Induced Lipoprotein Clearance in Cyp7b1-Deficient Mice.

  PMID 35478959 · PMC9038073 · Frontiers in cell and developmental biology · 2022 · 7 claims · 8 setups

  Has reproduction · 83

  Cyp7b1 deficiency blunts cold-induced hepatic Cyp7b1 upregulation and plasma bile acid synthesis

  liver plasma interscapular bat qrt-pcr western bile

• pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

  PMID 31114675 · PMC6505635 · F1000Research · 2019 · 7 claims · 4 setups

  Has reproduction · 90

  pysradb provides a command-line interface to query metadata and download raw sequencing data from NCBI SRA using the SRAdb SQLite database.

  sra-deposited pc3 sra tissues metadata polya assays

• Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

  PMID 33722289 · PMC7962346 · Genome biology · 2021 · 7 claims · 8 setups

  Has reproduction · 66

  A three-base-pair (HDR) or single-base (PE2) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder, but not heart or brain

  tissues zygotes aorta spleen qrt-pcr allele-specific restriction

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity.

  PMID 26695075 · PMC4687855 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction

  Hepatocyte apoE is required for normal VLDL production and protects against diet-induced dyslipidemia

  liver plasma pooled real-time western elisa

• The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

  PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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  The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

  genomic predicted cdna tissues genomic sequence pcr

• 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

• Positive selection for the male functionality of a co-retroposed gene in the hominoids.

  PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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  PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

  african chimpanzee orangutan reconstructed population hka comparative

• Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

  PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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  A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

  dog predicted ace3 panel blast sequence homology