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).

• Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis.

  PMID 41862476 · PMC13004862 · Nature communications · 2026 · 7 claims · 8 setups

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  Mechanical stress (MS) signaling is significantly elevated in endothelial cells (ECs) from IPF patients and correlates with fibrosis severity and lung function decline

  lung cd31+ single-nucleus scissor meta-analysis

• Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing.

  PMID 41875869 · PMC13030979 · Cell reports methods · 2026 · 8 claims · 8 setups

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  Nuclei isolation protocol is a critical experimental variable shaping snRNA-seq data quality and biological interpretation

  cortex brain cortical snrna-seq snrna-seq bright-field nuclei

• Single-cell resolution of an open chromatin signature in persister tumor cells.

  PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

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  Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

  non-malignant same epithelial tumor single-nucleus mitochondrial copy-number

• Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.

  PMID 42010880 · PMC13096584 · Aging cell · 2026 · 8 claims · 8 setups

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  T cells are the immune cell population with the most pronounced transcriptomic alterations during liver aging

  liver nash cirrhotic hcc scrna-seq snrna-seq stereo-seq

• Cross-tissue atlas of mucosa-associated lymphoid tissue lymphomas reveals intratumoral heterogeneity and microenvironmental subtypes.

  PMID 42066772 · PMC13198276 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Integrative bulk, single-nucleus, and spatial RNA-seq analysis identifies three LME subtypes in MALT lymphoma: LME1 (mesenchymal), LME2 (inflammatory), and LME3 (depleted).

  malt ffpe snrna-seq-derived snrna-seq bulk single-nucleus spatial

• Single-nucleus ATAC-seq analysis resolves chromatin and transcriptional features of fibrolamellar carcinoma.

  PMID 41865105 · PMC13144680 · Scientific reports · 2026 · 8 claims · 5 setups

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  snATAC-seq resolves cell-type specific chromatin accessibility, microRNA activity, transcription factor networks, and super enhancer usage in FLC tumors versus non-malignant liver (NML).

  flc bulk snatac-seq snrna-seq single-nucleus bulk motif

• A Cross-Species Single-Cell Atlas Reveals Conserved Regulatory Networks and Candidate Hearing Loss Genes in the Cochlea.

  PMID 42074555 · PMC13115875 · Genes · 2026 · 8 claims · 8 setups

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  A cross-species single-cell/single-nucleus RNA-seq atlas of human fetal and mouse postnatal cochlea identifies 19 conserved major cell types

  cochlea fetal top scrna-seq snrna-seq cell-cell

• Single-cell and spatial transcriptomics define 20E-driven developmental reprogramming in silkworm wing disc.

  PMID 41730863 · PMC13039787 · Nature communications · 2026 · 8 claims · 7 setups

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  Wing morphogenesis (Wm) cells act as central progenitors/differentiation hub, giving rise to epithelial and cuticle lineages under lineage-specific transcription factors

  mori spodoptera scrna-seq stereo-seq snrna-seq

• Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

  PMID 41675057 · PMC12886552 · iScience · 2026 · 8 claims · 6 setups

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  Grin2b+/C456Y mice show large-scale, age-dependent brain transcriptomic changes, peaking at 4 weeks postnatally

  brain hippocampus neuronal bulk trade gene

• Characterizing gene perturbations in single cells via network divergence analysis.

  PMID 41965857 · PMC13249949 · Nature communications · 2026 · 8 claims · 8 setups

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  scDNS quantifies gene-specific functional perturbations by measuring Jensen-Shannon divergence between condition-specific gene interaction network configurations

  ipsc-derived embryonic panc-1 triple scrna-seq single-nucleus

• Classification of ALS molecular subtypes: a literature review on machine learning applications and their clinical value.

  PMID 41731547 · PMC13037183 · BMC medicine · 2026 · 8 claims · 5 setups

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  Unsupervised ML analysis of ALS transcriptomes consistently identifies molecular subtypes reflecting distinct biological processes, primarily oxidative stress (ALS-Ox) and glial activation/neuroinflammation (ALS-Glia), found in every study reviewed.

  post-mortem peripheral bulk rna-seq blood