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

• DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency.

  PMID 31722211 · PMC6856714 · Cell reports · 2019 · 7 claims · 6 setups

  Has reproduction · 50

  The altered 3D genome of 2i-cultured ESCs (chromatin decompaction and loss of polycomb interactions at polycomb targets) is due to redistribution of polycomb away from its targets.

  ring1b− e3.5 e14 3b3l fluorescence fish situ

• Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

  PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

  genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

• Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

  PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

  Full-text index only

  Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

  csf brain normal 2d-dige label-free isotopic

• 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

• Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.

  PMID 30576656 · PMC6310685 · Molecular cell · 2018 · 8 claims · 8 setups

  Has reproduction

  Depletion of Rap1 induces divergent noncoding transcription at a large fraction of Rap1-regulated gene promoters

  cerevisiae rap1-aid northern western poly

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.

  hymenophyllum dark-adapted annotated differentially bulk relative chlorophyll

• Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

  PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

  Full-text index only

  277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

  umbilical ucb zebrafish microarray fluorescence-activated quantitative

• Nitrosative stress-induced s-glutathionylation of protein disulfide isomerase leads to activation of the unfolded protein response.

  PMID 19773442 · PMC2756322 · Cancer research · 2009 · 7 claims · 8 setups

  Full-text index only

  PABA/NO treatment causes S-glutathionylation (not S-nitrosylation) of PDI in cells and in vitro

  skov3 recombinant mtt daf-fm-da immunoprecipitation

• Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.

  PMID 41860215 · PMC13101498 · Applied and environmental microbiology · 2026 · 7 claims · 6 setups

  Has reproduction · 81

  DOM composition changes significantly across the nearshore-to-offshore transect, with more terrestrially derived and high-molecular-weight DOM nearshore, despite only minor reductions in DOC and similar inorganic N and P levels.

  free-living bacterioplankton 0.2-µm lake metatranscriptomics metagenomics dissolved

• Gene Regulatory Interactions at Lamina-Associated Domains.

  PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

  Has reproduction · 31

  Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

  adipose ascs mesenchymal chip-seq rna-seq atac-seq

• Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

  PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

  Has reproduction · 55

  RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

  amir-sul col 14-day-old arabidopsis small rna-seq gel

• Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle.

  PMID 32523568 · PMC7261829 · Frontiers in microbiology · 2020 · 6 claims · 6 setups

  Has reproduction · 97

  Photosynthesis-related and translational transcripts are upregulated at midday (high light) compared to night/darkness in the pond microeukaryotic community

  microeukaryotic phytoplankton pond filtered metatranscriptomics accessory situ

• 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

• Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

  PMID 12615897 · PMC2193825 · The Journal of experimental medicine · 2003 · 8 claims · 8 setups

  Full-text index only

  Artemis-deficient ES cells are severely impaired in VDJ coding joining but retain relatively normal RS (signal) joining

  recombined southern rt-pcr colony

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

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

  Full-text index only

  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

• A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.

  PMID 30332484 · PMC6192621 · PloS one · 2018 · 7 claims · 8 setups

  Has reproduction · 63

  The CGCG element (consensus TCTCGCGAGA) is a conserved 10-bp motif enriched in TATA-less, CpG island-associated promoters of ribosomal protein and housekeeping genes.

  k562 hek293t motif luciferase bidirectional

• Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

  PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum

  sycon ciliatum sponges differential go-term genome

• 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