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 126

Assay: beta ✕ Clear

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

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Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

lncap androgen prostate itraq mudpit immunoblot
Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

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10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

aorta cardiovascular peripheral blood methylation mirna expression
QUANT: a long-term multi-city commercial air sensor dataset for performance evaluation.

PMID 39168987 · PMC11339295 · Scientific data · 2024 · 7 claims · 7 setups

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The QUANT dataset is the most extensive open-access evaluation of commercial air quality sensor systems on a global scale to date

main wider maqs low-cost reference-grade meteorological
Calculating expected DNA remnants from ancient founding events in human population genetics.

PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

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Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

simulated forward-based size
An empirical study of choosing efficient discriminative seeds for oligonucleotide design.

PMID 19958494 · PMC2788383 · BMC genomics · 2009 · 8 claims · 3 setups

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The spaced seed is the most efficient discriminative seed for oligonucleotide design among the five algorithms tested.

simulated pmoa nirs seed
Correlations between gut microbiota and serum metabolomics in patients with neurogenic rosacea.

PMID 40676500 · PMC12272963 · BMC microbiology · 2025 · 6 claims · 3 setups

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Patients with neurogenic rosacea exhibit significant gut microbiota dysbiosis compared to healthy controls

serum fecal paired lc-ms 16s spearman
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

Has reproduction · 53

spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

bistable three-gene emt circuits simulation mixed-state grn
Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

hla-b44 plasma macrophages complement proteomics shotgun cap
Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

PMID 7669582 · PMC2033876 · British journal of cancer · 1995 · 8 claims · 5 setups

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A novel missense mutation (TGG→CGG, Trp133→Arg) in nm23-H2 was found in one stage III serous ovarian carcinoma

ovarian case matched same pcr-sscp subcloning loh
The interleukin 12 p40 gene promoter is primed by interferon gamma in monocytic cells.

PMID 8551218 · PMC2192398 · The Journal of experimental medicine · 1996 · 8 claims · 8 setups

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IFN-gamma primes phagocytic cells for LPS-induced transcription of the IL-12 p40 gene rather than directly inducing it

pbmc cell-depleted raw264.7 nuclei ria immunoprecipitation rnase
Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

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Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

synovial ss-derived normal liver rt-pcr cloning densitometric
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 80

BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr
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
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Computational verification of protein-protein interactions by orthologous co-expression.

PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time
Guar gum and similar soluble fibers in the regulation of cholesterol metabolism: current understandings and future research priorities.

PMID 19183750 · PMC2605338 · Vascular health and risk management · 2008 · 8 claims · 8 setups

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Soluble fiber consumption consistently reduces plasma total and LDL cholesterol in animal models and human clinical trials

guinea rats type healthy plasma clinical meta-analysis
Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

monocyte-derived mdm mdms western p24 seldi-tof sds-page

Experiments

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

QUANT: a long-term multi-city commercial air sensor dataset for performance evaluation.

Calculating expected DNA remnants from ancient founding events in human population genetics.

An empirical study of choosing efficient discriminative seeds for oligonucleotide design.

Correlations between gut microbiota and serum metabolomics in patients with neurogenic rosacea.

spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

The interleukin 12 p40 gene promoter is primed by interferon gamma in monocytic cells.

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

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

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Computational verification of protein-protein interactions by orthologous co-expression.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

Guar gum and similar soluble fibers in the regulation of cholesterol metabolism: current understandings and future research priorities.

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.