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 15

System / cell line: wild-type ✕ Assay: spatial ✕ Clear

Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer.

PMID 41907400 · PMC13018967 · iScience · 2026 · 8 claims · 8 setups

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Colorectal cancer fibroblast heterogeneity can be distilled into two overarching, transcriptomically distinct CAF populations marked by PDGFRA+ and ACTA2+ expression

crc colonic gemm scrna-seq multiplex bulk
Dissecting glioblastoma risk signatures in the tumor immune microenvironment based on multi-dimensional transcriptomics.

PMID 41880523 · PMC13154832 · GigaScience · 2026 · 7 claims · 8 setups

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Hallmarks of malignancy and cell cycle regulatory pathways are consistently enriched across single-cell, bulk, and spatial transcriptomic modalities, promoting tumor cell proliferation and progression.

tumor gbm normal wild-type single-cell bulk microarray
Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 67

Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

single methanol-fixed reads slice mrna-seq light-microscopy read
Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

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cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

discoideum single-cell scrna-seq dissecting
Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

crc epcam+ aggregated cancer scrna-seq copy pseudobulk
Neuronal Small RNAs Control Behavior Transgenerationally.

PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups

Has reproduction · 49

Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations

elegans prab-3 dissected worms small sequencing facs
Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

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The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

elegans whole-genome rnase pharmacological
A combined approach exploring gene function based on worm-human orthology.

PMID 15877817 · PMC1112593 · BMC genomics · 2005 · 8 claims · 6 setups

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Strict phylogenetic criteria (concordant Neighbor Joining and Maximum Parsimony tree topology) can select single most-likely human orthologs for C. elegans genes despite the large phylogenetic distance between worm and human sequences.

sapiens elegans hela phylogenetic rnai gfp
FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

Has reproduction · 73

Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

tnbc geo breast frmd8 bulk meta-analysis single-cell
Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

PMID 36203191 · PMC9535882 · BMC biology · 2022 · 8 claims · 8 setups

Has reproduction · 65

Comparative RNA-seq of cells isolated from central, intermediate, and peripheral regions of stage-3 embryos identifies genes with locally restricted expression genome-wide

tepidariorum drosophila rna-seq whole-mount parental
Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

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Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic
Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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Mutations in GLE1, an mRNA export mediator, cause LCCS1

lccs1 laahd finnish healthy genomic microsatellite carrier
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
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson

Experiments

Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer.

Dissecting glioblastoma risk signatures in the tumor immune microenvironment based on multi-dimensional transcriptomics.

Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

Neuronal Small RNAs Control Behavior Transgenerationally.

Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

A combined approach exploring gene function based on worm-human orthology.

FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

Rete ridges form via evolutionarily distinct mechanisms in mammalian skin.

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.