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 consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.

  PMID 24586345 · PMC3929608 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 59

  A de novo transcriptome for Calanus finmarchicus was assembled from six developmental-stage libraries, yielding 206,041 contigs and a reference set of 96,090 unique comps, representing a new molecular resource for this species.

  calanus pooled raw combined bulk extraction read

• 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

• Cis-regulatory evolution shapes facial diversity in birds and mammals.

  PMID 42090501 · PMC13148318 · Science advances · 2026 · 8 claims · 6 setups

  Full-text index only

  Mesenchymal populations show markedly greater transcriptomic/regulatory divergence between mouse and chicken than ectodermal populations, pointing to a central role of mesenchyme in shaping facial morphology

  embryo chicken embryos single-cell situ cross-species

• Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

  PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

  gastrulating gastrula gold-standard embryo single-cell computational promoter

• The RNA-binding protein SRSF3 controls epicardial formation by regulating splicing and proliferation.

  PMID 41601313 · PMC13006530 · Development (Cambridge, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  SRSF3 is highly expressed in the proepicardial organ and early epicardium, declining after E11.5 and remaining low postnatally

  embryo heart e11.5 proepicardium immunofluorescence qrt-pcr conditional

• Distal enhancers regulate mammalian early embryonic lineage differentiation through long-range interactions.

  PMID 41562256 · PMC12820533 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  Lineage-specific H3K27ac is predominantly enriched at distal enhancers rather than promoters, indicating first-lineage differentiation relies on distal enhancer activity

  pre-implantation low-cell-number 8-cell zygotes cut&tag atac-seq sequencing

• Toward a Consensus in the Repertoire of Hemocytes Identified in Drosophila.

  PMID 33748138 · PMC7969988 · Frontiers in cell and developmental biology · 2021 · 8 claims · 8 setups

  Has reproduction · 74

  Comparative analysis of three scRNAseq studies identifies eight common, robust hemocyte subgroups associated with distinct functions (proliferation, immune response, phagocytosis, secretion)

  wandering feeding stage type single scenic immunolabeling

• Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.

  PMID 38918881 · PMC11373658 · G3 (Bethesda, Md.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  Improved E. guineensis genome assembly achieved with substantially increased continuity and completeness compared to prior assemblies

  guineensis oleifera root pacbio proximity optical