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 94

Assay: pseudotime ✕ Clear

An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

Has reproduction · 88

SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

kidney tubuloids immunodeficient tub rt-qpcr western histology
Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

PMID 41458999 · PMC12738925 · Frontiers in bioinformatics · 2025 · 8 claims · 6 setups

Has reproduction · 64

Celline is a Python package that automates the full scRNA-seq workflow (retrieval, metadata extraction, preprocessing, cell-type annotation, batch correction, trajectory inference) via single-line commands.

c57bl embryonic scrna-seq quality cell-type
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

Has reproduction · 83

170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

afb1 breast training candidate computational bulk weighted
EpCAM supports exit from pluripotency of embryonic stem cells via Eomes.

PMID 41963283 · PMC13076738 · Cell death & disease · 2026 · 8 claims · 8 setups

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EpCAM supports exit from pluripotency of mESCs and is required for cardiomyocyte formation in embryoid bodies

e14tg2α epcam embryos mesc flow contraction qrt-pcr
A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

tcga-gbm glioma meta consensus wgcna machine
Multimodal single-cell protein and RNA profiling unveils dysregulated immature neutrophil dynamics in gestational diabetes mellitus.

PMID 41501166 · PMC12936121 · Communications biology · 2026 · 8 claims · 6 setups

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A combination of CD10−CD49d+Igκ+ surface markers identifies an immature low-density neutrophil (LDN) subset that is distinct from CD10+ mature high-density neutrophils (HDNs)

peripheral facs-sorted decidua pregnant infinityflow conventional may-grünwald
Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations.

PMID 41520091 · PMC12905261 · Communications biology · 2026 · 8 claims · 8 setups

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18 B cell subpopulations were identified spanning the full developmental continuum from early progenitors to plasma cells, including 4 previously unappreciated minor subpopulations (FTLhi, S100A8hi immature; FOShi, HSPA1Ahi naïve).

in-house enriched tonsil peripheral scrna-seq scvdj-seq velocity
Rtf1-dependent transcriptional pausing regulates cardiogenesis.

PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

zebrafish embryo embryonic mescs crispr situ shrna
Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

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BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

colorectal colon patients bulk single-cell spatial bulk
Endothelial stem cells of the retinal vasculature reside in the optic nerve.

PMID 41577708 · PMC12830651 · Nature communications · 2026 · 8 claims · 8 setups

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CD157+CD201+ endothelial stem cells (VESCs) reside predominantly in the optic nerve and supply endothelial cells to the retina

cd45negcd31+ sorted retina procr[cd201]-creert2 flow colony-forming flat-mount
An in vivo and in vitro spatiotemporal profile of human midbrain development.

PMID 41633979 · PMC12877092 · Nature communications · 2026 · 8 claims · 6 setups

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By 22 post-conceptional weeks (PCW), fetal ventral midbrain tissue exhibits structural complexity comparable to adult tissue

fetal ipsc-derived dopamine immunohistochemistry immunofluorescence droplet-based
VISTA drives pancreatic tumor progression through modulation of the tumor-associated macrophage polarity.

PMID 41776161 · PMC13194722 · Nature communications · 2026 · 8 claims · 8 setups

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VISTA deficiency significantly impairs PDAC tumor growth and prolongs survival in murine orthotopic models

pan02 cd45+ tumor mice orthotopic pharmacological flow
Precancerous niche remodelling dictates nascent tumour persistence.

PMID 41781610 · PMC13148994 · Nature · 2026 · 8 claims · 8 setups

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Newly emerging tumours actively remodel their surrounding stroma into a 'precancerous niche' that determines their long-term survival.

upper nascent oesophagus carcinogen-free immunofluorescence edu immune
Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

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A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

tcga-blca blca paired wgcna differential machine

Experiments

An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

EpCAM supports exit from pluripotency of embryonic stem cells via Eomes.

A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

Multimodal single-cell protein and RNA profiling unveils dysregulated immature neutrophil dynamics in gestational diabetes mellitus.

Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations.

Rtf1-dependent transcriptional pausing regulates cardiogenesis.

Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

Endothelial stem cells of the retinal vasculature reside in the optic nerve.

An in vivo and in vitro spatiotemporal profile of human midbrain development.

VISTA drives pancreatic tumor progression through modulation of the tumor-associated macrophage polarity.

Precancerous niche remodelling dictates nascent tumour persistence.

Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.