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).

Publications 1.3k Datasets 392.5k Experiments 852

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Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.

PMID 41537454 · PMC12805614 · The Journal of pathology · 2026 · 6 claims · 7 setups

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snRNA-seq identifies a novel tenogenic heterologous differentiation program (SCX, MKX, TNMD) in an endometrial carcinosarcoma

ffpe sections tumor cs4 single-nucleus immunohistochemistry fluorescence
Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion.

PMID 41540035 · PMC12808753 · Nature communications · 2026 · 8 claims · 7 setups

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A CRISPR screening platform combining human myoblast models, a custom muscle-targeted gRNA library (MyoCRISPR-KO Lib), and a split-toxin selection system enables quantitative enrichment of fusion-defective myocytes.

myoblasts myoblast time-course immunostaining gene
OTX2 inhibits human pluripotent stem cell reprogramming toward 8-cell-like and morula-like states.

PMID 41554740 · PMC12909843 · Nature communications · 2026 · 8 claims · 8 setups

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OTX2 establishes a repressive barrier to the induction of 8CLCs from primed hPSCs

tprx1-egfp otx2-ko primed preimplantation flow bulk single-cell
S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning.

PMID 41556263 · PMC13042551 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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S3RL is a separable representation learning framework that denoises sparse spatial transcriptomic data and enhances biologically relevant signals by integrating gene expression, spatial coordinates, and histological image features.

dorsolateral dlpfc nanostring spatial cell-type multi-platform
Dynamic single-cell transcriptomics reveals lsamp-guided neural network formation in male S. japonicum driving female reproduction.

PMID 41571647 · PMC12905319 · Nature communications · 2026 · 8 claims · 8 setups

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Generated a high-resolution single-cell transcriptomic atlas of 104,671 cells from male and female S. japonicum across four developmental stages, identifying 76 distinct cell populations

dissociated japonicum reproductive gscs single-cell fluorescence-activated whole-mount
Repeatability of gene expression evolution in experimental environmental adaptation.

PMID 41587990 · PMC12946262 · Nature communications · 2026 · 6 claims · 8 setups

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Gene expression evolution during experimental adaptation is far more repeatable across replicate populations than expected by chance, whether measured by shared DEGs, shared direction of change, or shared direction plus magnitude of change

coli yeast fly copepod microarray rna-seq
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-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity.

PMID 41593306 · PMC12868835 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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Innate antibacterial defense functions are generally enhanced in most cell types at AS onset and are negatively associated with AS severity

pbmcs gwas pbmc-derived cd4+ single-cell bulk mendelian
Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

PMID 41620539 · PMC12916760 · Scientific reports · 2026 · 8 claims · 9 setups

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76 overlapping genes were identified between COPD-associated DEGs and oxidative stress-related genes.

lung genecards differentially bronchial bulk database functional
FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

prostate targeted single-nucleus scatac-seq
Pharmacological perturbation of splicing elicits SMG1 reduction: Implications for cancer therapy.

PMID 41623476 · PMC12857400 · iScience · 2026 · 7 claims · 12 setups

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Splicing-modulatory drugs MS023 and indisulam act as inadvertent NMD inhibitors by downregulating SMG1 protein levels

4t1 tumor-draining arst panc02 mts tumor ifn-γ
Hypoxia-Induced Osteopontin-Positive Glioma-Associated Macrophages Facilitate Glioma Mesenchymal Transition via NF-κB Pathway Activation.

PMID 41625475 · PMC12857759 · Cancer communications (London, England) · 2026 · 6 claims · 8 setups

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A subset of GAMs with elevated OPN expression accumulates in response to hypoxic stimulation

thp-1 glioma orthotopic gbm bulk single-cell spatial
A single microRNA miR-195 rescues the arrested B cell development induced by EBF1 deficiency.

PMID 41649478 · PMC12880805 · eLife · 2026 · 8 claims · 8 setups

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Mir195 transduction rescues Ebf1-deficient HPCs, inducing CD19 expression and a B-lineage gene expression program

wild-type ebf1 nog mir195 flow cdna engraftment
BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

escs esc scrna-seq cellchat differential
Genomic biomarkers of immunotherapy plus chemotherapy in patients with advanced NSCLC: Insights from the phase 3 ORIENT-11 study.

PMID 41660271 · PMC12876322 · iScience · 2026 · 8 claims · 8 setups

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A 9-gene Immune-Chemotherapy Prediction Score (ICPscore), derived from ORIENT-11 via WGCNA and LASSO Cox regression, predicts survival benefit from ICI plus chemotherapy in advanced NSCLC

orient-11 hub nsclc oak bulk pd-l1 wgcna
Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

luad demtdmrgs gse131907 wgcna kegg univariate
ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression.

PMID 41688464 · PMC13018553 · Nature communications · 2026 · 8 claims · 8 setups

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ATRX deficiency downregulates α-globin (HBM/HBA) selectively in a subset of cells that exhibit DNA damage, rather than uniformly across the population

cd34+ single day hudep-2 crispr-cas9 cfu single-cell
Integrin β1 Demarks Precursors of Brain-Residing Antibody-Secreting Cells in Multiple Sclerosis.

PMID 41698162 · PMC12912196 · Neurology(R) neuroimmunology & neuroinflammation · 2026 · 7 claims · 6 setups

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ITGB1 (integrin β1/CD29) is a major transcriptomic and protein-level discriminator of CXCR3+ memory B cells in blood

facs-sorted pbmcs blood single-cell spectral transmigration
Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

PMID 41699006 · PMC13002898 · Scientific reports · 2026 · 8 claims · 8 setups

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CDC20, PLK1, BUB1, CDC45, and CDCA5 are concordantly identified as hub genes across seven NCBI-GEO datasets and the Pakistani RNA-seq dataset

pakistani pdac overlapping tcga-paad bulk functional protein-protein
Integrative bulk and single-cell transcriptomics link EZH2 to immunosuppressive programs and tumor-Treg crosstalk in castration-resistant prostate cancer.

PMID 41710887 · PMC12909565 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Higher EZH2 expression is associated with adverse clinical outcomes in bulk PCa/CRPC cohorts

tcga-prad su2c gse264573 gse137829 bulk scrna-seq ligand-receptor

Experiments

Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.

Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion.

OTX2 inhibits human pluripotent stem cell reprogramming toward 8-cell-like and morula-like states.

S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning.

Dynamic single-cell transcriptomics reveals lsamp-guided neural network formation in male S. japonicum driving female reproduction.

Repeatability of gene expression evolution in experimental environmental adaptation.

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

Single-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity.

Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

Pharmacological perturbation of splicing elicits SMG1 reduction: Implications for cancer therapy.

Hypoxia-Induced Osteopontin-Positive Glioma-Associated Macrophages Facilitate Glioma Mesenchymal Transition via NF-κB Pathway Activation.

A single microRNA miR-195 rescues the arrested B cell development induced by EBF1 deficiency.

BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

Genomic biomarkers of immunotherapy plus chemotherapy in patients with advanced NSCLC: Insights from the phase 3 ORIENT-11 study.

Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression.

Integrin β1 Demarks Precursors of Brain-Residing Antibody-Secreting Cells in Multiple Sclerosis.

Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

Integrative bulk and single-cell transcriptomics link EZH2 to immunosuppressive programs and tumor-Treg crosstalk in castration-resistant prostate cancer.