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 Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer

• Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.

  PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 75

  Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes

  arabidopsis bulk hierarchical gene

• Gata-3 and mammary cell fate.

  PMID 17381824 · PMC1868924 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

  Full-text index only

  Gata-3 is required for formation of mammary placodes during embryonic development

  mammary gata-3 k14-cre mmtv-cre microarray lacz cre

• Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells.

  PMID 41507516 · PMC12880982 · Communications biology · 2026 · 8 claims · 6 setups

  Full-text index only

  Hypoxia induces a coordinated downregulation of mito-nuclear OXPHOS gene expression across most human cell lines tested

  hct-116 u87 h460 hif1α rna-seq qpcr chip-seq

• TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

  PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

  Has reproduction · 80

  TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

  imr90 hct116 chip-seq rna-seq atac-seq

• Innate antiviral and immune functions associated with the HIV reservoir decay after anti-PD-1 therapy.

  PMID 41680482 · PMC12920136 · Nature medicine · 2026 · 7 claims · 7 setups

  Full-text index only

  Anti-PD-1 therapy triggers a rapid (within 24 hours) systemic cascade of increased IFN/antiviral, monocyte, and CD8+ T cell effector transcriptomic modules alongside decreased plasma TGFβ.

  pbmcs plasma pbmc publicly bulk plasma integrated

• Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

  PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

  Has reproduction · 73

  FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

  peripheral white four gse75360 microarray gene weighted

• Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

  PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

  Has reproduction · 93

  24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

  jatropha geo bulk semi-quantitative quantitative

• Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

  PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another

  scrna-seq tcga-gbm gse131928 tumor gene pairwise principal

• A Statistical Framework for Measuring Reproducibility and Replicability of High-Throughput Experiments From Multiple Sources.

  PMID 41636474 · PMC12871010 · Statistics in medicine · 2026 · 8 claims · 3 setups

  Full-text index only

  nestedIDR, a nested copula mixture model, extends the IDR framework to multi-lab studies by jointly modeling within-lab reproducibility and between-lab replicability

  simulated encode seqc simulation chip-seq rna-seq