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).

• 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

• PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

  PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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  PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

  pah scrna-seq pah-former candidate scrna-seq transfer perturbation

• Microglia maintain structural integrity during fetal brain morphogenesis.

  PMID 38309258 · PMC10869139 · Cell · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  Embryonic ATM-like microglia accumulate at two fetal cortical boundaries, the cortico-striato-amygdalar boundary (CSA) and cortico-septal boundary (CSB), resembling post-natal axon-tract-associated microglia (ATM)

  embryonic cx3cr1 fetal embryos single-cell immunolabeling phrodo

• RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

  PMID 36429012 · PMC9688714 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 37

  RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression

  brain rna-edited brain-isolated naïve rna-seq pathway pcr

• 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

• Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication.

  PMID 41719185 · PMC12937581 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  Tensor-cell2cell v2 implements a non-negative coupled tensor component analysis (CTCA) that jointly factorizes protein- and metabolite-mediated communication tensors sharing context, sender, and receiver dimensions while keeping ligand-type-specific (private) dimensions separate.

  cortical paired single-cell protein-mediated metabolite-mediated

• Hepatocyte dedifferentiation in 2D culture reveals extensive transcriptomic and proteomic rewiring.

  PMID 41111196 · PMC12506984 · Hepatology communications · 2025 · 8 claims · 3 setups

  Has reproduction · 77

  2D culturing of primary hepatocytes for 24 hours causes extensive transcriptomic (>10,000 genes) and proteomic (>3000 proteins) rewiring compared with freshly isolated cells

  c57bl same bulk quantitative single-nucleus

• Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

  PMID 41563441 · PMC13007207 · Diabetes · 2026 · 8 claims · 7 setups

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  5′ single-cell library preparation protocols outperform 3′ protocols for transcript identification and read length

  lines pancreatic spleen dtc single-cell bulk ngs

• Epigenetic regulation of serine biosynthesis by PHF8 during neurogenesis.

  PMID 41714361 · PMC13022353 · EMBO reports · 2026 · 8 claims · 8 setups

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  PHF8 is required for neural stem cell (NSC) proliferation in vitro

  developing nscs embryonic single-cell shrna growth

• Distinct radial glia subtypes regulate midbrain dopaminergic neuron development.

  PMID 41699318 · PMC13061605 · Nature neuroscience · 2026 · 8 claims · 8 setups

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  Rgl1 is the progenitor of the mesDA neuronal lineage

  embryonic developing wa09 bulk scrna-seq ligand-receptor

• H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity.

  PMID 40764058 · PMC12487818 · Genome research · 2025 · 8 claims · 8 setups

  Has reproduction · 55

  H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding

  imefs early ctcf h3k9me3 h3k9me2

• Biphasic expression of thyroid hormone receptor TRβ1 in mammalian retina and anterior ocular tissues.

  PMID 37033230 · PMC10076699 · Frontiers in endocrinology · 2023 · 7 claims · 8 setups

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  TRβ1 shows a biphasic, late-peaking expression profile in retina that contrasts with the early embryonic peak of TRβ2

  retina fetal retinal cones rna-seq lacz immunofluorescence

• Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

  PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

  Has reproduction · 100

  Molecular techniques such as RT-PCR only allow detection of known viruses, with each test specific to one or a small number of related viruses, so unknown viruses can be missed

  garlic pepper pear grapevine rna-seq srna-seq

• Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development.

  PMID 41577697 · PMC12932823 · Nature communications · 2026 · 8 claims · 6 setups

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  DOE-based multifactorial screening combined with bulk RNA-seq comparison to scRNA-seq pharyngeal atlases identifies signaling factors that optimize iPSc differentiation toward thymic epithelial progenitors (TEPs)

  ipsc embryonic ipsc-derived bulk scrna-seq qpcr

• Alternative splicing-triggered mRNA decay informs splice-switching targets for neurodevelopmental disorders.

  PMID 41678398 · PMC13078869 · The Journal of clinical investigation · 2026 · 7 claims · 12 setups

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  EANMD, a new computational tool, identifies AS-NMD exons using the 50 nt rule plus additional transcript-level features and outperforms existing tools (SpliceTools, NMD Classifier)

  neuro2a embryonic e14.5 cortical rna-seq pacbio rt-pcr

• Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset.

  PMID 41807428 · PMC13103403 · Scientific data · 2026 · 8 claims · 4 setups

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  A paired scRNA-seq and scATAC-seq dataset was generated from NPCs differentiated over Days 0, 7, 13, and 20 under baseline and Aβ 1-42 exposure conditions

  hipsc-derived hippocampal scrna-seq scatac-seq flow

• Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.

  PMID 31515287 · PMC6771397 · Genome research · 2019 · 7 claims · 6 setups

  Has reproduction · 75

  XCR during iPSC reprogramming is hierarchical, with distinct subsets of X-linked genes reactivating early, intermediate, late, and very late

  mus mefs bulk independent allele-specific fluorescence-activated live

• Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

  PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  >700 tissue-specific transcriptomes generated from w1118 and 141 DGRP Drosophila lines, forming a circadian gene expression atlas

  w1118 dgrp drosophila dgrp-796 bulk high uas-rnai

• Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR.

  PMID 41771837 · PMC12953643 · Signal transduction and targeted therapy · 2026 · 8 claims · 8 setups

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  KLF15 transcriptional activity shows the most significant change among TFs in pathological cardiomyocytes during progressive hypertrophic remodeling, reflecting less effective repression of disease-associated genes.

  ventricular heart cardiomyocytes cardiomyocyte single-cell rt-qpcr bulk

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  ChIRP-MS of SARS-CoV-2 RNA in infected Huh7.5 and Vero E6 cells identifies a comprehensive set of 309 host proteins that bind the viral RNA during active infection

  huh7.5 vero schmidt lung chirp-ms chirp-rna-seq sds-page