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).

• UBE2M as a bridge spanning neddylation and cell cycle regulation in colorectal adenocarcinoma.

  PMID 41680469 · PMC12993059 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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  Neddylation is associated with G2M phase progression in CRC

  crc paired hek293t cell-free single-cell bulk immunohistochemistry

• PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.

  PMID 41556358 · PMC13042517 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  A PRDM1+ malignant epithelial cell subcluster (Epi_C4) is enriched in NMPR patients and is associated with nICRT treatment resistance

  locally escc pd-1 kyse-30 single-arm scrna-seq bulk

• Prior-guided factorization for reliable imputation of scRNA-seq data.

  PMID 41860953 · PMC13004523 · PLoS computational biology · 2026 · 8 claims · 8 setups

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  scZN models scRNA-seq counts as a mixture of a two-state (Gamma-Poisson/negative binomial) transcriptional bursting process and dropout, formalized via a zero-inflated negative binomial (ZINB) and solved as constrained nonnegative matrix factorization into a cell-to-cell-type assignment matrix and a cell-type expression matrix

  ercc real randomly brain scrna-seq cell-cycle k-nn

• 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

• Development of double-positive thymocytes at single-cell resolution.

  PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups

  Has reproduction · 86

  DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d

  thymocytes sorted thymocyte scrna-seq flow immunofluorescence

• A Novel Human Cellular System for Studying Normal Aging and for Anti-Aging Discovery.

  PMID 41556081 · PMC12816977 · Aging cell · 2026 · 6 claims · 8 setups

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  In vitro hTSC-derived STBs recapitulate in vivo CTB-STB maturation and major cellular aging features, including multinucleation, hormone secretion, cell cycle arrest, genome instability, epigenetic changes, transposable element activation, and SASPs.

  peri-implantation first-trimester term-stage musc scrna-seq bulk linear

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of published mouse and human scRNA-seq experiments through a user-friendly interface.

  randomly single-cell single scrna-seq cell-type orthogonal

• Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

  PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

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  GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

  upd gsc-like wild-type scrna-seq differential gene

• Discovery and Evaluation of Biomarkers for Triple-Negative Breast Cancer Subtypes Uncovers Patient Stratification and Targeted Therapeutic Strategies.

  PMID 41671401 · PMC13176827 · Cancer research · 2026 · 7 claims · 8 setups

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  A set of basal identity genes (SMA/ACTA2, TAGLN, TPM2) defined by scRNA-seq analysis enables subclassification of TNBC into a subgroup termed true basal TNBC (tB-TNBC)

  healthy ffpe tcga i-spy2 scrna-seq immunohistochemistry bulk

• The GENEVA platform models tumor mosaicism to reveal variations of responses to KRAS inhibitors and identify improved drug combinations.

  PMID 41735640 · PMC13035475 · Nature cancer · 2026 · 8 claims · 8 setups

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  GENEVA is a scalable single-cell-resolution platform for measuring drug responses across genetically diverse pooled 2D/3D cultures and xenograft models

  pooled pool nsg mosaic scrna-seq crispri mitotracker

• Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response.

  PMID 41728950 · PMC12926921 · Nucleic acids research · 2026 · 5 claims · 8 setups

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  CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain overall gene expression

  mcf-7 rpe1 mcf-7-dcas9 tissue-wide isoform-specific reanalysis qrt-pcr

• Single-cell RNA-sequencing highlights a curtailed NK cell function in convalescent COVID-19 pregnant women.

  PMID 40661959 · PMC12257036 · Frontiers in immunology · 2025 · 7 claims · 5 setups

  Has reproduction · 87

  NK cells show a sustained reduction during active SARS-CoV-2 infection and persisting after recovery in pregnant women

  pbmcs serum 14-color single-cell 13-plex

• TRAP5 Inhibition Targeting Scar-Associated Macrophages Ameliorates Acute Kidney Injury to Chronic Kidney Disease Transition.

  PMID 41773735 · PMC13159109 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  A distinct scar-associated macrophage (SM) subset marked by high Acp5/TRAP5, Ctsk, Mmp9, and Spp1 emerges and predominates during the renal remodeling/CKD phase after AAI-induced AKI

  kidney ckd aai unilateral single-cell velocity pseudotime

• Annexin A13 Protects Against Acute Kidney Injury by Inactivating TGF-β/Smad3 Signaling.

  PMID 41486854 · PMC12915081 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  ANXA13 is selectively downregulated in the kidneys of AKI patients and IRI- or cisplatin-induced AKI mice, primarily in proximal tubular cells

  kidney aki renal hek293t rna-seq immunohistochemistry serum

• scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

  PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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  scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

  single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type

• Glioblastoma invasion into different organoid hosts reveals cell-intrinsic and proliferative migratory programs.

  PMID 41959666 · PMC13059114 · iScience · 2026 · 8 claims · 8 setups

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  GB cells invade both neural and endodermal organoid hosts (lineage-independent), whereas non-malignant neural progenitor cells show markedly reduced infiltration

  gbm1 gfp-gbm1 facs-sorted post-invasion image-based immunofluorescence single-cell

• Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location.

  PMID 41637132 · PMC12872174 · eLife · 2026 · 8 claims · 6 setups

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  Transcriptomic clustering of wing disc cells groups mainly based on proximodistal (PD) cell location, in both irradiated and unirradiated conditions.

  drosophila immunofluorescence edu single-cell

• Genetic evidence supporting obesity as a risk factor for lung squamous cell carcinoma and the identification of MFAP1 as a shared genetic target.

  PMID 41820721 · PMC13096280 · Discover oncology · 2026 · 8 claims · 8 setups

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  BMI and LUSC show a significant positive genome-wide genetic correlation, robust to constrained-intercept sensitivity analysis and replicated by GNOVA.

  gwas gtex scrna-seq ldsc gnova ρ-hess

• Targeting KIFC1 to disrupt centrosome clustering and trigger anaphase catastrophe in small-cell lung cancer.

  PMID 41948931 · PMC13134724 · JCI insight · 2026 · 8 claims · 8 setups

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  KIFC1 is overexpressed in SCLC compared with normal tissues and other cancer types

  sclc h146 clinical cancer immunofluorescence viability flow

• An optimized protocol for efficient derivation of pancreatic islets from multiple human pluripotent stem cell lines.

  PMID 41997152 · PMC13163220 · Stem cell reports · 2026 · 8 claims · 8 setups

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  Shortening the S4 pancreatic progenitor stage duration enhances subsequent S5 endocrine progenitor (EP) differentiation efficiency

  hs980 hpsc-derived eight sc-islets flow static dynamic