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).

• Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.

  PMID 37012284 · PMC10070245 · Scientific reports · 2023 · 7 claims · 8 setups

  Has reproduction · 90

  Batch correction using sequencing platform as the correcting variable (via Combat-Seq) removes technical variability so that samples cluster by injury condition rather than dataset origin.

  zebrafish orthologs ortholog core bulk overrepresentation network

• Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

  PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

  zebrafish computational seven consolidated whole-adult-organism supervised quantitative

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation

• ECgene: an alternative splicing database update.

  PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

  nine genome sage cdna genome-based chi-squared sage

• TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes.

  PMID 35580127 · PMC9159589 · PLoS genetics · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Pigmentation genes are only expressed in mitfa-expressing zebrafish melanocyte-lineage cells that also express tfap2 paralogs

  gfp+ sk-mel-28 tfap2a single-cell crispr atac-seq

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 6 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22.

  mus tissues liver-specific kidney bulk microarray chip-seq

• Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

  PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

  post-mortem brain zebrafish bulk single-cell unsupervised

• Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.

  PMID 17855401 · PMC2094075 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  LDSS analysis identifies octamer sequences with localized distribution profiles as promoter constituents, classifiable into groups (REG, TATA, Inr, Kozak, CpG, Y Patch)

  arabidopsis rice promoter cross-species ldss sequence distribution

• PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

  PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

  sequences poly cdna trace pssm-based

• Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

  PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

  aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr

• Chromosomal phenotypes and submicroscopic abnormalities.

  PMID 15601540 · PMC3525070 · Human genomics · 2004 · 8 claims · 8 setups

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  Microdeletion syndromes are flanked by region-specific low-copy repeats (LCRs), and non-allelic homologous recombination (NAHR) between these LCRs, via interchromosomal or intrachromosomal mechanisms, causes the deletions.

  patients parents vegf164 zebrafish breakpoint parental inversion

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic