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 identification of a Distinct Astrocyte Subtype that Diminishes in Alzheimer's Disease.

  PMID 38502590 · PMC11567244 · Aging and disease · 2024 · 7 claims · 7 setups

  Has reproduction · 57

  A distinct astrocyte subpopulation marked by low GFAP, AQP4+, and CD63+ expression exists in normal brain and is functionally enriched for Aβ clearance and tau protein binding

  hippocampus prefrontal astrocyte frontal single-nuclei gene cell-cell

• Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.

  PMID 41576947 · PMC12985369 · Cell genomics · 2026 · 7 claims · 7 setups

  Full-text index only

  snRNA-seq census of 227,680 nuclei across 48 cell types reveals altered cellular states and compositional rewiring of the distal lung in ILD

  frozen lung flash-frozen spatial single-nucleus scrna-seq 10x

• Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

  PMID 41507195 · PMC12881518 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  A multi-omics strategy combined with TWAS reveals brain-region-specific molecular signatures and striking gene dysregulation concentrated in inhibitory neurons in an FXTAS mouse model.

  brain prefrontal pfc gabaergic bulk single-nuclei immunofluorescent

• Cellular insights into transposable elements in Alzheimer's disease.

  PMID 41573740 · PMC12819740 · Frontiers in molecular biosciences · 2025 · 8 claims · 5 setups

  Full-text index only

  508 TE loci are differentially expressed in AD brain, with the large majority (84.3%) upregulated, indicating widespread TE activation

  postmortem brain genome genes single-nucleus atac-seq pseudobulk

• Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility.

  PMID 41638211 · PMC13091097 · Cell systems · 2026 · 8 claims · 7 setups

  Full-text index only

  A complex, intact gut microbiome is necessary for the steady-state transcriptional landscape of all major brain-resident cell types, with myelinating oligodendrocytes and immune cells showing the largest microbiome-dependent transcriptional response.

  hippocampus cd11b+ intestinal brain single-nucleus bulk multiplex

• Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

  PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

  Full-text index only

  Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

  substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 90

  Multi-omic profiling (snRNA-seq + spatial transcriptomics) of human sural nerves identifies novel cell type markers (MLIP in mySC; GRIK3, PRIMA1 in nmSC; CXCL14 in periC) not previously described in rodent or human literature

  sural peripheral snrna-seq nerve single-nucleus subcellular situ

• Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

  PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

  Has reproduction · 84

  MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

  patient-derived tumor single paired single-nucleus infercnv aracne-ap

• An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

  PMID 41937210 · PMC13067603 · Genome biology · 2026 · 8 claims · 8 setups

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  Constructed an integrated multiomic atlas of the human left ventricle combining ~2.3M snRNA-seq nuclei from 299 donors and ~690K snATAC-seq nuclei from 106 donors

  left heart cardiac snrna-seq snatac-seq bulk

• A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

  PMID 42030938 · PMC13198283 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A multiomic (snRNA-seq, snATAC-seq, WGS, CODEX) atlas defines a core set of pHGG neoplastic cell states shared across molecular subtypes

  phgg neoplastic fetal single-nucleus whole-genome codex

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

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

  Full-text index only

  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

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• Transcriptomic study of WSSV infection in Litopenaeus vannamei lymphoid organ via single nuclei RNA sequencing.

  PMID 42044139 · PMC13119866 · PloS one · 2026 · 6 claims · 3 setups

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  A novel nuclei isolation protocol optimized for shrimp tissues was developed to enable single nuclei RNA-sequencing (snRNA-seq) of the lymphoid organ.

  lymphoid shrimp vannamei single qpcr pathogen

• 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

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

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

  Full-text index only

  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

• Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.

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

  Full-text index only

  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

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 million formalin-fixed single-cell single-nucleus integrated

• Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

  PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

  pancreatic kpc pdac tcga-paad rna-seq bulk proteomics

• 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

  Full-text index only

  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