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).

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.

  PMID 34140473 · PMC8211662 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 90

  The human post-implantation epiblast transitions from a naïve to a primed pluripotent state, with naïve markers (KLF4, KLF17, PRDM14, etc.) downregulated and primed markers (FGF2, DNMT3B, SOX11, etc.) upregulated between pre- and post-implantation stages

  embryo embryos single-cell logistic immunofluorescence

• Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.

  PMID 17557180 · PMC1998882 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 7 claims · 7 setups

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  A BAC transgene containing Prop1 completely rescues the Prop1 mutant (dwarf) phenotype, showing all necessary regulatory elements lie within the BAC

  pig lemur cv-1 b-prop1 bac comparative transient

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

  PMID 41612263 · PMC12924552 · BMC biology · 2026 · 8 claims · 6 setups

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  Profiling gene expression across 26 life stages of A. millepora and building an interactive Shiny-based tool (DEView) enables comprehensive visualisation of developmental transcriptomic data.

  acropora millepora bulk differential pca

• Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

  PMID 36203191 · PMC9535882 · BMC biology · 2022 · 8 claims · 8 setups

  Has reproduction · 65

  Comparative RNA-seq of cells isolated from central, intermediate, and peripheral regions of stage-3 embryos identifies genes with locally restricted expression genome-wide

  tepidariorum drosophila rna-seq whole-mount parental

• Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

  PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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  A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

  genome candidate gxd medline evolutionary gene expression

• Genomics--from Neanderthals to high-throughput sequencing.

  PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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  Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

  bacterial ion-channel drosophila arrays next-generation pooled multiplex

• Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

  PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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  Mutations in GLE1, an mRNA export mediator, cause LCCS1

  lccs1 laahd finnish healthy genomic microsatellite carrier

• auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.

  PMID 36078102 · PMC9454499 · Cells · 2022 · 8 claims · 7 setups

  Has reproduction · 50

  auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD)

  fish genomic auts2 tissues comparative tblastn phylogenetic

• Genomic organization of zebrafish microRNAs.

  PMID 18510755 · PMC2427041 · BMC genomics · 2008 · 8 claims · 6 setups

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  Using sequence conservation and prediction algorithms, 35 new zebrafish miRNAs were identified, bringing the total to 415.

  zebrafish candidate hairpin blast secondary comparative

• An ancient genome duplication event drives the development and evolution of spinnerets in spiders.

  PMID 41533794 · PMC12802834 · Science advances · 2026 · 8 claims · 8 setups

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  A single whole-genome duplication (WGD) event occurred in the Arachnopulmonata stem lineage during the Silurian (~438 Ma), supported by macrosynteny, Ks distributions, and WHALE gene-tree reconciliation.

  luthela chelicerate arachnid gene chromosome-scale phylogenomics macrosynteny