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).

• The proteomic landscape and temporal dynamics of human and mouse gastruloid development.

  PMID 42032312 · PMC13179132 · Nature cell biology · 2026 · 8 claims · 8 setups

  Full-text index only

  Generated a quantitative proteomic, phosphoproteomic, and matched transcriptomic resource across four stages of human and mouse gastruloid development

  escs gastruloids sox2-mcitrine quantitative phosphoproteomics bulk

• Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

  PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

  mda-mb231 epithelial breast early-stage cdna quantitative facs

• Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

  PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

  Full-text index only

  Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

  hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna

• Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.

  PMID 42010620 · PMC13227897 · Journal of neuroinflammation · 2026 · 8 claims · 5 setups

  Full-text index only

  Morphine-dependent macaques show increased CD4+ TCM and Treg cell proportions and decreased CD8+ TEM cell proportions in CSF at the pre-infection timepoint compared to saline controls

  csf scrna-seq necropsy single-cell flow cell-cell

• A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

  PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

  crc epithelial rcrc tcga-read scrna-seq copy gene

• Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

  PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  Endothelial cell-specific deletion of Adgrl2 impairs cerebrovascular integrity in mice

  wild-type cortex brain single-molecule single-cell immunohistochemistry

• Placental gene signatures associated with high neonatal adiposity: role for immune cell activation.

  PMID 41958865 · PMC13061145 · Journal of the Endocrine Society · 2026 · 8 claims · 8 setups

  Full-text index only

  A placental transcriptomic signature is associated with high neonatal adiposity

  placental term atlas neonates bulk gene protein-protein

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 8 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share a transcriptional overlap of 239 unique common differentially expressed genes (DEGs), 237 of which are up-regulated

  patients pbmcs plasma derived bulk single-cell quantitative

• Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

  PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity

  lung c57bl pbmcs macrophages bulk metabolomics histopathology

• Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

  PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

  Full-text index only

  Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

  liver hepg2 293t serum bulk single-cell oil

• Decoding unchanged transcriptome of Alzheimer's disease reveals an NCAM1 mRNA switch as a potential biomarker.

  PMID 42006342 · PMC13090632 · iScience · 2026 · 8 claims · 7 setups

  Full-text index only

  Most genes are gene-level non-differentially expressed (nDEGs) in AD but nDEGs are strongly associated with neuronal function pathways

  hippocampus brain bulk alternative isoform