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).

• Transcriptional responses to proteotoxic stressors are profoundly diverse and tissue-specific.

  PMID 41619802 · PMC12908066 · Cell stress & chaperones · 2026 · 8 claims · 7 setups

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  Heat shock, HSP90 inhibition, and polyQ aggregation launch fundamentally distinct RNA expression programs rather than a shared stress response.

  muscle q175 striatum gene bulk enrichr principal

• 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

• 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

• Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

  PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups

  Has reproduction · 75

  Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.

  testes normal gene rna-seq sapas cdna

• Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

  PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

  stricta long-read short-read hi-c

• Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability.

  PMID 41946711 · PMC13233917 · Nature communications · 2026 · 8 claims · 8 setups

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  Single-oocyte full-length (PacBio long-read) isoform sequencing systematically profiles isoform diversity across human (GV, MI, MII) and mouse (GV, GVBD, MI, MII) oocyte maturation stages

  oocytes oocyte pacbio isoform comparative