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).

• Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies.

  PMID 41503158 · PMC12770963 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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  A comprehensive comparison of seven 3'/whole-transcriptome single-cell platforms and two 5' whole-transcriptome + TCR platforms was performed using PBMCs from multiple donors.

  pbmcs sorted scrna-seq evercode

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn

• High-quality acinar cell isolation enables single-cell analysis of healthy and injured pancreas.

  PMID 42013858 · PMC13198085 · Cell reports methods · 2026 · 8 claims · 7 setups

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  The DCTC protocol isolates up to 90% acinar cells from healthy wild-type pancreatic tissue without cell fixation or dead-cell removal kits

  healthy pancreas epithelial kpc scrna-seq pseudobulk velocity

• Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data.

  PMID 41825449 · PMC13030991 · Cell reports methods · 2026 · 7 claims · 3 setups

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  NCLUSION matches the performance of state-of-the-art single-cell clustering techniques with significantly reduced runtime

  brain-large scdesign3-simulated facs-purified scrna-seq simulated

• Single-Cell Differential Network Analysis with Sparse Bayesian Factor Models.

  PMID 35186014 · PMC8855158 · Frontiers in genetics · 2021 · 8 claims · 2 setups

  Has reproduction · 85

  A hierarchical Bayesian factor model using treatment-dependent latent factor loadings can construct gene co-expression networks from scRNA-seq data and identify differences in network structure between two (or more) biological conditions.

  simulated sars-cov-2 scrna-seq

• Cell fixation and preservation for droplet-based single-cell transcriptomics.

  PMID 28526029 · PMC5438562 · BMC biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  Methanol fixation stabilizes and preserves dissociated cells for weeks without compromising single-cell RNA-seq data quality

  hek293 dissociated facs-sorted hek drop-seq bulk trizol

• Autophagy Activators Normalize Aberrant Tau Proteostasis and Rescue Synapses in Human Familial Alzheimer's Disease iPSC-Derived Cortical Organoids.

  PMID 41591759 · PMC13042409 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 7 setups

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  An optimized CO differentiation protocol (Protocol 2, using 50% E6/50% hESC medium with constant rocking/orbital shaking) produces reproducible, larger, lower-necrosis organoids with consistent size across genotypes

  isogenic scrna-seq fixed cos single-cell pseudotime immunofluorescence

• Single cell snapshot analyses under proper representation reveal that epithelial-mesenchymal transition couples at G1 and G2/M.

  PMID 41611829 · PMC12894973 · Communications biology · 2026 · 7 claims · 8 setups

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  TGF-β induced EMT in MCF10A cells follows two broad paths that arise from coupling between cell cycle and EMT at either the G1 or G2/M phase

  mcf10a scrna-seq vector pseudotime

• 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

• Chikungunya virus persists in joint-associated macrophages and promotes chronic disease in mice.

  PMID 41922840 · PMC13171603 · Nature microbiology · 2026 · 8 claims · 7 setups

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  Inflammatory macrophages accumulate in joint-associated tissue during the chronic stage of CHIKV infection and show an activated, pro-inflammatory, MHC-II+ transcriptional programme

  ankle ipsilateral computational pfa-fixed rt-qpcr single-cell gene

• Cell-State-Specific Drug Responses are Associated With Differences in Signaling Network Wiring.

  PMID 41707849 · PMC13014938 · Molecular & cellular proteomics : MCP · 2026 · 8 claims · 4 setups

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  Drug treatment effects propagate from the EGF-signaling pathway to other connected parts of the cellular signaling network, indicating altered signaling flow.

  epidermal single-cell scrna-seq immuno-staining