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).

• Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

  PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups

  Has reproduction · 68

  viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.

  transgenic elegans four gfp genetic template-independence

• Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

  PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

  Has reproduction · 64

  L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

  elegans small small sequencing lifespan

• Bidirectional CRISPR screens decode a GLIS3-dependent fibrotic cell circuit.

  PMID 41501466 · PMC12820784 · Nature · 2026 · 8 claims · 8 setups

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  Inflammation-associated fibroblasts (IAFs), induced by proinflammatory FCN1+IL1B+ macrophages, produce profibrotic IL-11 and drive fibrosis in IBD

  intestinal colon pdgfra+ colonic scrna-seq xenium masson's

• RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

  PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

  hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq

• Genetic evidence supporting obesity as a risk factor for lung squamous cell carcinoma and the identification of MFAP1 as a shared genetic target.

  PMID 41820721 · PMC13096280 · Discover oncology · 2026 · 8 claims · 8 setups

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  BMI and LUSC show a significant positive genome-wide genetic correlation, robust to constrained-intercept sensitivity analysis and replicated by GNOVA.

  gwas gtex scrna-seq ldsc gnova ρ-hess

• The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

  PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality

  non-coding frnadb-hosted genomic mammalian sequence genome blastn

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing

• Completing the map of human genetic variation.

  PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

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  A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

  genomic fosmid full hapmap paired targeted genotyping

• Deep-learning prediction of gene expression from personal genomes.

  PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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  Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

  gtex rosmap same monocyte paired mutagenesis chromhmm

• Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution.

  PMID 41738738 · PMC12935429 · eLife · 2026 · 8 claims · 8 setups

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  LS-MPRA (BAC-based) and d-MPRA (systematic mutagenesis) are complementary methods for unbiased, high-resolution mapping of cis-regulatory modules.

  mus e14 retina candidate ls-mpra single-cell individual

• The application of genomic technology to combat parasitic disease.

  PMID 16454893 · PMC1914215 · Parasitology · 2004 · 8 claims · 8 setups

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  Genomic resources from mammalian hosts can be exploited to understand parasitic processes from the host's standpoint, illustrated by host cell penetration by Trypanosoma cruzi.

  trypanosoma toxoplasma parasite eimeria host proteomics comparative

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Autophagy Activators Normalize Aberrant Tau Proteostasis and Rescue Synapses in Human Familial Alzheimer's Disease iPSC-Derived Cortical Organoids.

  PMID 41591759 · PMC13042409 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 7 setups

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  An optimized CO differentiation protocol (Protocol 2, using 50% E6/50% hESC medium with constant rocking/orbital shaking) produces reproducible, larger, lower-necrosis organoids with consistent size across genotypes

  isogenic scrna-seq fixed cos single-cell pseudotime immunofluorescence