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).

• A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

  PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups

  Has reproduction · 69

  Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.

  mus chuniphyes hormiphora pleuromamma rna-seq homology

• Under the Shadow: Old-biased Genes Are Subject to Weak Purifying Selection at Both the Tissue- and Cell Type-Specific Levels.

  PMID 41092135 · PMC12569596 · Genome biology and evolution · 2025 · 7 claims · 6 setups

  Has reproduction · 93

  ADICT (age-related decrease in transcriptome conservation) is commonly found in ageing tissues of nonmammalian species, including chicken brain, killifish liver and skin, and fruit fly brain

  drosophila nothobranchius gallus heterocephalus bulk single-cell

• Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.

  PMID 31515287 · PMC6771397 · Genome research · 2019 · 7 claims · 6 setups

  Has reproduction · 75

  XCR during iPSC reprogramming is hierarchical, with distinct subsets of X-linked genes reactivating early, intermediate, late, and very late

  mus mefs bulk independent allele-specific fluorescence-activated live

• Exploring microproteins from various model organisms using the mip-mining database.

  PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups

  Has reproduction · 85

  Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions

  nine cerevisiae thaliana bulk transcriptome growth

• The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

  PMID 17145711 · PMC1751528 · Nucleic acids research · 2007 · 7 claims · 5 setups

  Full-text index only

  GermOnline is a cross-species systems browser providing comprehensive curated information on genes and gene products relevant for sexual reproduction across nine model organisms including human.

  saccharomyces mus rodent classical tiling comparative

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid

• Lineage-Specific Disruption of Hematopoiesis by Oxaliplatin: Mechanisms of Erythropoietin Resistance and Immune Suppression.

  PMID 41868970 · PMC13005433 · Journal of hematology and oncology research · 2026 · 8 claims · 5 setups

  Full-text index only

  Oxaliplatin induces coordinated, lineage-dependent suppression of hematopoiesis, strongest in erythroid and lymphoid lineages while neutrophils are relatively spared

  bone peripheral plasma bulk complete multiplex