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 23

System / cell line: morphology ✕ Assay: abundance ✕ Clear

Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.

PMID 14709176 · PMC395736 · Genome biology · 2003 · 8 claims · 5 setups

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Distinct cellular processes are coregulated by androgen while others are essentially unaffected in LNCaP cells

lncap computational icat western hypergeometric
Proteomics analysis of the expression of neurogranin in murine neuroblastoma (Neuro-2a) cells reveals its involvement for cell differentiation.

PMID 17505539 · PMC1865092 · International journal of biological sciences · 2007 · 6 claims · 5 setups

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Expression of Ng in Neuro-2a cells causes widespread down-regulation of microtubule components and associated proteins that mediate neurite outgrowth

neuro-2a hek293 icat western morphology
stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

PMID 41692960 · PMC12960910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

Has reproduction · 75

stDyer-image directly associates the image modality with predicted cluster labels rather than using images to enhance/impute gene expression data

non-small morphology brain breast spatial image
Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups

Has reproduction · 65

eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.

edna khumbu genome metabarcoding satellite
MitoP2: the mitochondrial proteome database--now including mouse data.

PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

saccharomyces yeast heart liver genome-wide single transcriptome
Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

PMID 18174378 · PMC2605348 · Blood · 2008 · 7 claims · 8 setups

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Homozygous SLC4A1 Ser667Phe mutation causes both hereditary spherocytosis and incomplete distal renal tubular acidosis in the proband

erythrocyte genomic erythrocytes xenopus sds-page sscp dids
Proteomics analysis of the nucleolus in adenovirus-infected cells.

PMID 19812395 · PMC2808258 · Molecular & cellular proteomics : MCP · 2010 · 7 claims · 5 setups

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SILAC-based quantitative MS identified 351 nucleolar proteins, with 24 showing at least a 2-fold change in abundance after adenovirus infection

hela silac gel maldi-tof
Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.

PMID 19794824 · PMC2753780 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 4 setups

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141 protein spots are differentially expressed between normal rat sera and MCA-induced lung cancer rat sera (82 overexpressed, 59 underexpressed)

serum lung excised two-dimensional maldi-tof-ms histopathology
Proteomic-based identification of maternal proteins in mature mouse oocytes.

PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

mature mii identified tissues sds-page acid gene
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
Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi.

PMID 19078957 · PMC2696133 · Nature · 2009 · 8 claims · 8 setups

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GNAQ is frequently somatically mutated in blue nevi (83%) and uveal melanoma (46%)

archival nevus htert melan-a sanger pna-clamp soft
Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups

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RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)

u937 saos-2 chip-chip chip-on-chip gene
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race
Cancer-cell-secreted miR-204-5p induces leptin signalling pathway in white adipose tissue to promote cancer-associated cachexia.

PMID 37620316 · PMC10449837 · Nature communications · 2023 · 8 claims · 8 setups

Has reproduction · 85

Breast cancer cell-secreted exosomal miR-204-5p induces HIF1A in white adipose tissue by targeting the VHL gene.

balb nsg ewat iwat orthotopic indirect sev
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups

Has reproduction · 65

comBO is a single iPSC-derived organoid differentiation that generates osteolineage, vascular, lymphoid, and myeloid compartments together

hipsc-derived combo combo-derived healthy-donor flow single-cell confocal
Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

Has reproduction · 64

The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

caecilian caecilia archival lws pcr eye histology
Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

PMID 17392682 · PMC2642915 · Molecular vision · 2007 · 8 claims · 8 setups

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MLF accumulation more closely reflects the onset of AMD than LF accumulation

donor arpe-19 mlf sucrose phototoxicity fluorescence
Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

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Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

saccharomyces higher yeast mitochondria genome-wide rnai gene
Phosphoproteomic analysis of human embryonic stem cells.

PMID 19664994 · PMC2726933 · Cell stem cell · 2009 · 8 claims · 6 setups

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MDLC-MS/MS phosphoproteomics identified 2546 phosphorylation sites on 1602 phosphoproteins in undifferentiated hESCs and their differentiated derivatives

esc hescs hesc-derived undifferentiated mdlc-ms immunocytochemistry western
Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.

PMID 37160956 · PMC10169776 · Scientific reports · 2023 · 7 claims · 8 setups

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Spontaneous ΦD5-resistant D. solani mutants DsR34 and DsR207 show significantly reduced virulence and colonization ability in planta compared to wild-type

potato solani planta maceration genome

Experiments

Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.

Proteomics analysis of the expression of neurogranin in murine neuroblastoma (Neuro-2a) cells reveals its involvement for cell differentiation.

stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

MitoP2: the mitochondrial proteome database--now including mouse data.

Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

Proteomics analysis of the nucleolus in adenovirus-infected cells.

Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.

Proteomic-based identification of maternal proteins in mature mouse oocytes.

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

Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi.

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

Cancer-cell-secreted miR-204-5p induces leptin signalling pathway in white adipose tissue to promote cancer-associated cachexia.

comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

Phosphoproteomic analysis of human embryonic stem cells.

Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.