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).

• Innate immune modulation by RNA viruses: emerging insights from functional genomics.

  PMID 18654572 · PMC7097543 · Nature reviews. Immunology · 2008 · 8 claims · 7 setups

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  Influenza virus signals primarily through RIG-I to induce ISG expression, while West Nile virus signals through both RIG-I and MDA5 cooperatively.

  embryonic liver brain serial gene-expression computational

• Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability.

  PMID 15778432 · PMC1067522 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Dinucleotide microsatellite alterations in human cancer fall into two distinct modes: Type A (length changes ≤6 bp) and Type B (changes ≥8 bp)

  msh2− mlh1− lymphomas colorectal fluorescent sequencing immunohistochemistry

• 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

• HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

  PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 66

  HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

  embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq

• Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

  PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  Endothelial cell-specific Adgrl2 deletion impairs cerebrovascular integrity (blood–brain barrier).

  p30 cortex brain single-molecule single-cell immunohistochemistry

• GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

  PMID 18795106 · PMC2532782 · Experimental diabetes research · 2008 · 6 claims · 4 setups

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  GeneSpeed Beta Cell is an online genomics data repository allowing simultaneous multiexperiment viewing and multidimensional (Boolean intersection/union) querying of pancreas- and islet-relevant datasets, integrated with GeneSpeed's domain-based gene categorization.

  embryonic pancreatic panel pituitary affymetrix

• TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.

  PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups

  Has reproduction · 78

  TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.

  embryonic trim28 mrna-seq trim28 h3k9me3

• Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

  PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

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  A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

  genomic hek293 m17 south sscp dual-luciferase pcr-rflp

• The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.

  PMID 36196618 · PMC9720673 · Development (Cambridge, England) · 2022 · 8 claims · 8 setups

  Has reproduction · 82

  Can-elt-3 (and orthologues in C. portoensis and C. monodelphis) is expressed in the early E lineage prior to elt-2 orthologue expression

  angaria elegans portoensis gata rnai single-molecule smifish

• Mosaicism in von Hippel-Lindau disease: an event important to recognize.

  PMID 18205710 · PMC4401302 · Journal of cellular and molecular medicine · 2007 · 7 claims · 5 setups

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  The proband's father is a somatic mosaic for a VHL missense mutation (R161Q), explaining his mild, late-onset phenotype compared to his daughter's severe early-onset disease.

  peripheral father's pcr proband dhplc sanger semiquantitative

• Neuronal Small RNAs Control Behavior Transgenerationally.

  PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups

  Has reproduction · 49

  Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations

  elegans prab-3 dissected worms small sequencing facs

• Optical mapping discerns genome wide DNA methylation profiles.

  PMID 18667073 · PMC2516518 · BMC molecular biology · 2008 · 6 claims · 3 setups

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  Methylated restriction sites can be identified in optical maps as cleavage sites that are absent relative to the in silico (sequence-based) restriction map, since most restriction enzymes fail to cut methylated cognate sequences.

  escherichia embryonic optical

• Genomic and proteomic techniques applied to reproductive biology.

  PMID 11574051 · PMC138959 · Genome biology · 2001 · 8 claims · 8 setups

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  Knockout of the E6-AP (UBE3A) gene reduces testis and prostate size in male mice and compromises estradiol action in females

  e6-ap fgf9-deficient jsd one-cell gene germ-cell interference

• Bacteriophage Mu integration in yeast and mammalian genomes.

  PMID 18953026 · PMC2602771 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  In vitro-assembled Mu transpososomes, delivered by electroporation, efficiently integrate marker genes into yeast, mouse ES, human HeLa, and human ES cell genomes

  cerevisiae ab2.2 hela fes29 electroporation southern transposition

• Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

  PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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  Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

  mcf7 arabidopsis specified different chip-seq microarray array-based

• DiRE: identifying distant regulatory elements of co-expressed genes.

  PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

  liver myod transgenic microarray tfbs enhancer

• CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

  PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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  CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

  cd4+ hela imr90 embryonic chip-seq computational gene

• A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

  PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

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  A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

  family k4425 embryonic scn9a-n641y linkage copy deletion

• Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain.

  PMID 15737014 · PMC549606 · PLoS medicine · 2005 · 7 claims · 6 setups

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  A secondary EGFR exon 20 mutation (T790M) is found in tumors from patients with acquired resistance to gefitinib or erlotinib

  tumor 293t nsclc direct fluorescent rt-pcr

• Use of functional genomics to understand influenza-host interactions.

  PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

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  Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

  hela a549 lung texas cdna microarray infection