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: normalized ✕ Assay: cell-type-specific ✕ Clear

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental
Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

Has reproduction · 75

Endothelial cell-specific deletion of Adgrl2 impairs cerebrovascular integrity in mice

wild-type cortex brain single-molecule single-cell immunohistochemistry
Epigenetic context defines the transcriptional activity of canonical and noncanonical NF-κB signaling in pancreatic cancer.

PMID 41844578 · PMC13039881 · Cell death discovery · 2026 · 8 claims · 8 setups

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TNFα is the primary activator of canonical NF-κB signaling via RELA in PDAC

pdac patient-derived aspc-1 l3.6pl single-cell bulk multiplex
Directing stem cell differentiation by chromatin state approximation.

PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

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Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr
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
Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna
Niacin promotes motor function recovery after spinal cord injury via Hcar2-dependent microglia immunometabolic regulation.

PMID 42068080 · PMC13135113 · Clinical and translational medicine · 2026 · 8 claims · 8 setups

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Hcar2 is a microglia-enriched gene whose spinal cord expression is upregulated after SCI, peaking at 7 days post-injury

spinal c57bl bv2 single-cell bulk sci
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

Has reproduction · 94

Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

nsclc coad brca tcga scrna-seq bulk rna-seq
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
EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

PMID 41832145 · PMC13133354 · Nature communications · 2026 · 8 claims · 7 setups

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EPInformer outperforms existing gene expression prediction models (Xpresso, CREaTor, Seq-GraphReg, Enformer, Borzoi) in rigorous 12-fold cross-chromosome validation for both RNA-seq and CAGE expression prediction

k562 lines likely cell-type-specific rna-seq cage abc
Placental gene signatures associated with high neonatal adiposity: role for immune cell activation.

PMID 41958865 · PMC13061145 · Journal of the Endocrine Society · 2026 · 8 claims · 8 setups

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A placental transcriptomic signature is associated with high neonatal adiposity

placental term atlas neonates bulk gene protein-protein
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.

PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 8 claims · 7 setups

Has reproduction · 100

Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p, Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic CRC sites compared to primary CRC.

pcrc same mli ngs mirna bioinformatics differential
Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

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Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

liver hepg2 293t serum bulk single-cell oil
Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

PMID 41939867 · PMC13043422 · Frontiers in immunology · 2026 · 7 claims · 8 setups

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CXCL13, IL33, TLR4, and IGF1 are core IPF genes consistently linked to immune infiltration and fibrotic remodeling across bulk, single-cell, spatial, and blood multi-omics data

lung candidate bulk normalized bulk ppi machine

Experiments

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

Epigenetic context defines the transcriptional activity of canonical and noncanonical NF-κB signaling in pancreatic cancer.

Directing stem cell differentiation by chromatin state approximation.

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

Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

Niacin promotes motor function recovery after spinal cord injury via Hcar2-dependent microglia immunometabolic regulation.

iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

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

EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

Placental gene signatures associated with high neonatal adiposity: role for immune cell activation.

A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.

Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.