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).

• De novo H3.3K27M-altered diffuse midline glioma in human brainstem organoids to dissect GD2 CAR T cell function.

  PMID 41492091 · PMC12948678 · Nature cancer · 2026 · 8 claims · 8 setups

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  FGF4 supplementation during organoid patterning specifically induces pontine/rostral hindbrain brainstem identity

  hes brainstem day developing bulk immunofluorescence scrna-seq

• Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.

  PMID 41493197 · PMC13110159 · Plant biotechnology journal · 2026 · 8 claims · 5 setups

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  An optimised Visium spatial transcriptomics protocol (two-step OCT embedding combined with OCT-Immersion First cryopreservation) preserves high-integrity RNA from fragile plant tissues such as SAM

  maize integrated spatial integrity dimensional

• Tachykinin signaling defines distinct populations of glia in the enteric nervous system.

  PMID 41512855 · PMC12832054 · Neuron · 2026 · 8 claims · 8 setups

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  Mucosal and muscularis glia are transcriptionally distinct populations, with mucosal glia resembling microglia and muscularis glia resembling satellite glia/astrocytes

  ileum gfp+ intestinal intestine bulk scrna-seq bayesprism

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat

• Single-cell and spatial transcriptomic profiling of cardiac fibroblasts following myocardial infarction.

  PMID 41526391 · PMC12890913 · Scientific data · 2026 · 7 claims · 6 setups

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  Cthrc1+ Reparative Cardiac Fibroblasts (RCFs) are the primary driver of the cardiac healing process after myocardial infarction

  col1α1-gfp+ heart frozen bulk single-cell spatial

• Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

  PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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  APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

  urothelial urothelial-specific ureter hek293t single-cell poly fluorescence

• Rtf1-dependent transcriptional pausing regulates cardiogenesis.

  PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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  Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

  zebrafish embryo embryonic mescs crispr situ shrna

• Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.

  PMID 41537454 · PMC12805614 · The Journal of pathology · 2026 · 6 claims · 7 setups

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  snRNA-seq identifies a novel tenogenic heterologous differentiation program (SCX, MKX, TNMD) in an endometrial carcinosarcoma

  ffpe sections tumor cs4 single-nucleus immunohistochemistry fluorescence

• Single-Cell Profiling Across Immune Tissues and Organs Reveals Immunosenescence Signatures in Male Rhesus Monkeys.

  PMID 41556329 · PMC13042567 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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  GZMB is markedly upregulated across multiple cell types in aged rhesus monkeys and serves as a candidate biomarker of immunosenescence

  bone cd8+ mesenteric sections single-cell gene pseudotime

• Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment.

  PMID 41556506 · PMC12818872 · eLife · 2026 · 8 claims · 8 setups

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  Mouse TM contains three molecularly distinct, reproducible cell subtypes (TM1, TM2, TM3) identified by scRNA-seq and validated by IF/ISH

  limbal lmx1b scrna-seq snatac-seq immunofluorescence

• Dynamic single-cell transcriptomics reveals lsamp-guided neural network formation in male S. japonicum driving female reproduction.

  PMID 41571647 · PMC12905319 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a high-resolution single-cell transcriptomic atlas of 104,671 cells from male and female S. japonicum across four developmental stages, identifying 76 distinct cell populations

  dissociated japonicum reproductive gscs single-cell fluorescence-activated whole-mount

• Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

  PMID 41578129 · PMC12932634 · NPJ breast cancer · 2026 · 8 claims · 7 setups

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  Identified 30 isolated tumor cells (ITCs) in a clinically metastasis-negative tumor-draining lymph node, representing the initial metastatic seeding event, spanning ~200 μm

  dissected same tumor xenium-derived bulk enzymatic whole-genome

• Tissue-resident macrophage and dendritic cells drive type I IFN immunity to enteroviruses in the liver.

  PMID 41592119 · PMC12858076 · PLoS pathogens · 2026 · 8 claims · 6 setups

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  Type I IFN signaling (Ifnar1), but not type III IFN signaling (Ifnlr1), is essential for survival and for limiting viral replication in the liver during echovirus infection

  neonatal liver survival viral h&e

• Systems biology of gene regulation fulfills its promise.

  PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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  Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

  unspecified embryonic five yeast chip-chip chip-pet computational

• An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

  PMID 19925645 · PMC2791104 · BMC bioinformatics · 2009 · 7 claims · 3 setups

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  The loop design compares three patients pairwise across three hybridizations instead of each patient against a normal reference, using all arrays for informative test samples and avoiding ambiguity from benign CNVs in a reference sample.

  genomic e.g array karyotyping fish

• Collisionless relaxation of a disequilibrated current sheet and implications for bifurcated structures.

  PMID 34145266 · PMC8213726 · Nature communications · 2021 · 6 claims · 4 setups

  Has reproduction · 95

  Collisionless transitions among four single-particle orbit classes are responsible for the relaxation/equilibration of a disequilibrated current sheet.

  disequilibrated harris earth's particle-in-cell single-particle spacecraft

• Chips to hits.

  PMID 11983055 · PMC139346 · Genome biology · 2002 · 8 claims · 8 setups

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  Illumina's fiber-optic bead array technology allows ~2,000 oligonucleotide-based assays per bead array for high-throughput genotyping

  individual yeast pools lncap cell-based affymetrix automated

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage

• Proteomics technologies and challenges.

  PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

  serum myeloid formalin-fixed general maldi-tof phage maldi

• Firefly genomes illuminate parallel origins of bioluminescence in beetles.

  PMID 30324905 · PMC6191289 · eLife · 2018 · 7 claims · 8 setups

  Has reproduction · 93

  Bioluminescence arose independently (parallel/convergent origins) in fireflies and click beetles rather than from a single common ancestral origin.

  photinus aquatica ignelater pyralis whole-genome linked-read gene