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).

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

  PMID 31515287 · PMC6771397 · Genome research · 2019 · 8 claims · 5 setups

  Has reproduction · 75

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

  mus embryonic reprogramming ipsc allele-specific fluorescence-activated live

• Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

  PMID 33837217 · PMC8035321 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 68

  MOCCI (encoded by C15ORF48) is a mito-SEP upregulated during inflammation and infection that promotes host-protective resolution

  aortic failing colon hek293t ribo-seq wgcna-gsea gene

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

  PMID 18397877 · PMC2427143 · Human molecular genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  All six somatic TSC1 missense mutations found in bladder tumours cause loss of TSC1 function, but via distinct molecular mechanisms.

  hcv29 lines tsc1 bladder immunoblotting real-time co-immunoprecipitation

• Recruitment of the m(6)A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

  PMID 39300486 · PMC11414060 · Genome biology · 2024 · 8 claims · 8 setups

  Has reproduction · 78

  ZBTB48 physically interacts with the m6A/m6Am demethylase FTO

  hek293 inducible polyadenylated ap-ms co-immunoprecipitation clip

• Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

  PMID 36373634 · PMC9723646 · Nucleic acids research · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells (OSCs)

  drosophila ovarian osc melanogaster chip-seq sirna western

• The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

  PMID 12381271 · PMC134458 · BMC genetics · 2002 · 7 claims · 8 setups

  Full-text index only

  UNC93A maps within the minimal region of allele loss on 6q27 between D6S264 and D6S149, centromeric to D6S149

  panel 293-t malignant same rt-pcr northern fluorescence

• NovelFam3000--uncharacterized human protein domains conserved across model organisms.

  PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

  lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining

• Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.

  PMID 35013236 · PMC8748982 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Aβ (APP/PS1) and Tau (MAPT P301S) pathology induce distinct but overlapping astrocyte translatome signatures

  astrocytes aldh1l1_egfp-rpl10a astrocyte ageing trap-seq immunofluorescence ribosome

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• 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

• Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

  PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

  Full-text index only

  Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

  saccharomyces higher yeast mitochondria genome-wide rnai gene

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

  PMID 28446242 · PMC5406893 · Genome medicine · 2017 · 7 claims · 6 setups

  Has reproduction · 92

  Breast tumors exhibit two discrete GFRN activity phenotypes: a 'survival phenotype' with concordant HER2/IGF1R/AKT activation and a 'growth phenotype' with concordant EGFR/KRAS(G12V)/RAF1/BAD activation, which are typically mutually exclusive.

  mammary tcga hmecs breast rna-sequencing pathway western

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm/pSHF via an evolutionarily conserved intronic enhancer.

  micro-dissected dissected e9.5 xenopus bulk rt-qpcr whole-mount

• Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis.

  PMID 32762840 · PMC7413667 · eLife · 2020 · 8 claims · 8 setups

  Has reproduction · 81

  mRNA localization to mitochondria is condition-dependent: ATP3 mRNA switches from low (diffuse) association in fermentative conditions to strong mitochondrial association in respiratory conditions, while TIM50 is constitutively localized and TOM22 is diffuse.

  cerevisiae computational live-cell single-molecule single-cell

• 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

  PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups

  Has reproduction · 78

  A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.

  interrogans canine syrian smrt bulk rt-qpcr

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

  triticum taiqd wheat promoter genome-wide phylogenetic synteny

• Neuronal Small RNAs Control Behavior Transgenerationally.

  PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups

  Has reproduction · 49

  Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations

  elegans prab-3 dissected worms small sequencing facs