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 14

System / cell line: enriched ✕ Assay: copy-number ✕ Clear

PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups

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PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.

hek293t pbmcs melanoma bone single-cell infercnv gene
An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

PMID 41577803 · PMC12920623 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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Inflammatory CAFs (iCAFs) predominate in LUAD, whereas myofibroblastic CAFs (mCAFs) predominate in LUSC

nsclc epithelial macrophage caf scrna-seq copy gene-set
Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

Has reproduction · 58

Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

strain jel427-p9 genes whole-genome snp indel
Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

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Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

gastric wgs paired genes whole-genome whole-transcriptome mutational
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

Has reproduction · 85

High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

breast er+ epithelial malignant scrna-seq spatial copy
To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

Has reproduction · 33

C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

coronary scrna-seq five type single-cell doublet copy
DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

PMID 42152108 · PMC13185202 · Genome medicine · 2026 · 8 claims · 5 setups

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Relatively simple ML models (logistic regression) outperform complex algorithms such as deep neural networks for methylation-based cancer classification

validation cns healthy genes methylation copy-number gene-set
TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

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TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated
Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

PMID 41364805 · PMC13012255 · Blood cancer discovery · 2026 · 7 claims · 8 setups

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IFN-γ signaling after autologous stem cell transplant (ASCT) is associated with markers of impaired CD8+ T-cell memory phenotype

cd138neg cd138pos bone cd8+ single-cell bulk whole-genome
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.

PMID 41535307 · PMC12913623 · Nature communications · 2026 · 8 claims · 8 setups

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e2MPRA, combining lentiviral integration-based MPRA with CUT&Tag or ATAC-seq, enables simultaneous measurement of regulatory activity, protein binding, and epigenetic modification of the same synthetic CRE sequences.

hepg2 lentimpra atac-seq h3k27ac
Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

PMID 41578129 · PMC12932634 · NPJ breast cancer · 2026 · 8 claims · 7 setups

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Identified 30 isolated tumor cells (ITCs) in a clinically metastasis-negative tumor-draining lymph node, representing the initial metastatic seeding event, spanning ~200 μm

dissected same tumor xenium-derived bulk enzymatic whole-genome
Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

PMID 32542016 · PMC7295234 · PloS one · 2020 · 7 claims · 8 setups

Has reproduction · 51

Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC compared to normal liver at mRNA and/or protein level

oncomine tcga-lihc gse89377 hcc pan-cancer bulk microarray
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

Has reproduction · 71

AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

aml hovon cancer tcga bulk consensus machine

Experiments

PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.

Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.