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 222

System / cell line: spatial ✕ Clear

Critical role for a high-plasticity cell state in lung cancer.

PMID 41565826 · PMC12960256 · Nature · 2026 · 8 claims · 8 setups

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The HPCS is a transcriptionally distinct cancer cell state that functions as a hub for reciprocal transitions between other cancer cell states

autochthonous kpfrt gfp+ sorted single-cell flow immunofluorescence
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
Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.

PMID 41593194 · PMC13004670 · Nature medicine · 2026 · 8 claims · 5 setups

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PD-1 blockade induces tumor-specific IgG1+ plasma cell responses that complement cellular immunity and contribute to clinical benefit

tumor paired single-cell bulk multiplex
The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

PMID 41625479 · PMC12857760 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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Neutrophils in the lung metastatic niche comprise two functionally distinct subsets, Ly6g^high and Ly6g^low, based on Ly6g expression level

lung cramp cd8+ neutrophils single-cell flow genetic
Rete ridges form via evolutionarily distinct mechanisms in mammalian skin.

PMID 41639458 · PMC12959975 · Nature · 2026 · 8 claims · 8 setups

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Rete ridges form through a mechanism independent from hair follicles and sweat glands, via interconnected epidermal invaginations

trunk pig multispecies gw12 histology comparative immunostaining
Vertebrate-wide transcriptomic screening identifies immune cell-specific expression of the conserved OR-κ gene.

PMID 41654976 · PMC13113109 · Zoological letters · 2026 · 8 claims · 8 setups

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The majority (95-97%) of chemoreceptor genes are expressed in nasal/oral chemosensory organs across mouse, Xenopus, Polypterus, and zebrafish

mus zebrafish xenopus polypterus bulk single-cell molecular
Single-cell transcriptomic analysis of plant quiescent center by third-generation sequencing reveals developmental trajectories.

PMID 41664205 · PMC12990480 · Genome biology · 2026 · 8 claims · 8 setups

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Developed an improved protoplasting/hand-picking protocol enabling isolation of intact QC cells for single-cell long-read RNA sequencing (SCAN-seq)

arabidopsis single-cell rt-pcr agarose
Base barrier cells provide compartmentalization of choroid plexus, brain and CSF.

PMID 41680326 · PMC12971494 · Nature neuroscience · 2026 · 8 claims · 8 setups

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A distinct fibroblast population, ChP base barrier cells (BBCs, formerly type II fibroblasts), exists at the base of the choroid plexus, separate from ChP stromal (type I) fibroblasts

lateral brain mesp1-cre chp scrna-seq multiplex immunofluorescence
Heterozygous ADAR mutant mice exhibit RNA sensing-dependent neuroinflammation and phenotypes associated with Aicardi-Goutières syndrome.

PMID 41704749 · PMC12907846 · iScience · 2026 · 8 claims · 8 setups

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A heterozygous Adar G1007R (mouse G956R/G567) mouse model recapitulates the genetic and inflammatory features of human ADAR G1007R AGS patients

brain computational coronal adar1 real-time bulk ingenuity
Unveiling critical signaling pathways in the murine salivary gland and the role of midkine.

PMID 41732276 · PMC12925232 · iScience · 2026 · 8 claims · 6 setups

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CellChat analysis of scRNA-seq data from E12, E14, and E16 murine SMG reveals distinct and evolving ligand-receptor signaling networks across developmental stages

submandibular smg e13.5 single immunofluorescence organ
Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila.

PMID 41735587 · PMC12987734 · Nature genetics · 2026 · 8 claims · 8 setups

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Pico-C, a low-input Micro-C method, enables high-resolution, temporally resolved 3D genome mapping in early Drosophila embryos using as few as ~60,000 nuclei

hand-staged early drosophila pico-c chip-seq atac-seq
Multi-modal skin atlas identifies a multicellular immune-stromal community associated with disrupted cornification and specific T cell expansion in atopic dermatitis.

PMID 41741455 · PMC13057205 · Nature communications · 2026 · 8 claims · 8 setups

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Generated a multi-modal single-cell atlas of 280,518 cells from 27 samples/17 adults (healthy, AD non-lesional/lesional, scleroderma), integrated with 430,186 cells from four prior studies into a 710,704-cell human skin atlas with 86 annotated granular cell subsets.

skin healthy keratinocytes re-annotated droplet-based scrna-seq bulk
Benchmarking LLM-based agents for single-cell omics analysis.

PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

agent single-cell spatial scatac-seq llm-agent scrna-seq spatial
Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.

PMID 41776501 · PMC13162433 · Molecular cancer · 2026 · 8 claims · 6 setups

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MeRLin, a single-vector high-complexity lineage tracing platform integrating cellular barcoding, scRNA-seq, RNA-FISH, and computational analysis, was developed to track clonal and transcriptional dynamics in a melanoma PDX model

wm4237-1 nsg bulk scrna-seq clonal
A hormetic transcriptional program coregulates invasion, proliferation and dormancy to define metastatic potential.

PMID 41781391 · PMC13077004 · Nature communications · 2026 · 8 claims · 7 setups

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Prrx1 is a master regulator of dissemination that, beyond promoting invasion, represses proliferation (via Ccnd1/2, Cdkn2a/b/c) and activates a dormancy program (Gas6, Mme, Ogn)

infiltrating metabric facs-sorted pymt immunohistochemistry bioinformatic rt-qpcr
Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups

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SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival

pdac bulk ssgsea differential
Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

PMID 41807578 · PMC13230996 · Molecular systems biology · 2026 · 7 claims · 8 setups

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CSI-TME is a computational pipeline that deconvolves bulk tumor RNA-seq into cell-type-specific expression (via CODEFACS), infers transcriptional states per cell type via ICA, and identifies IC pairs from two cell types whose joint activity is associated with survival via Cox regression

idh-mutant tcga cgga deconvolved scrna-seq bulk independent
Optimisation of the core subset for the APY approximation of genomic relationships.

PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

Has reproduction · 85

APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

simulated real genotyped gblup population
Lung scRNA-seq reveals chronic inflammation and emphysemous phenotype in mice with osteogenesis imperfecta.

PMID 41822759 · PMC12978693 · Frontiers in genetics · 2026 · 8 claims · 3 setups

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Aga2 mice show increased alveolar spacing (emphysematous phenotype) at postnatal day 28 (p28) but not at p5

lung histology single-cell rnascope
DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

PMID 41761000 · PMC13043845 · Discover oncology · 2026 · 8 claims · 8 setups

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Neuroactive ligand–receptor signaling is among the most significantly upregulated pathways in LUAD relative to normal lung tissue.

tcga-luad tcga luad dendritic-cell bulk survival pan-cancer

Experiments

Critical role for a high-plasticity cell state in lung cancer.

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

Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.

The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

Rete ridges form via evolutionarily distinct mechanisms in mammalian skin.

Vertebrate-wide transcriptomic screening identifies immune cell-specific expression of the conserved OR-κ gene.

Single-cell transcriptomic analysis of plant quiescent center by third-generation sequencing reveals developmental trajectories.

Base barrier cells provide compartmentalization of choroid plexus, brain and CSF.

Heterozygous ADAR mutant mice exhibit RNA sensing-dependent neuroinflammation and phenotypes associated with Aicardi-Goutières syndrome.

Unveiling critical signaling pathways in the murine salivary gland and the role of midkine.

Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila.

Multi-modal skin atlas identifies a multicellular immune-stromal community associated with disrupted cornification and specific T cell expansion in atopic dermatitis.

Benchmarking LLM-based agents for single-cell omics analysis.

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.

A hormetic transcriptional program coregulates invasion, proliferation and dormancy to define metastatic potential.

Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

Optimisation of the core subset for the APY approximation of genomic relationships.

Lung scRNA-seq reveals chronic inflammation and emphysemous phenotype in mice with osteogenesis imperfecta.

DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.