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: muscle ✕ Assay: relative ✕ Clear

Induction of calcification by serum depletion in cell culture: a model for focal calcification in aortas related to atherosclerosis.

PMID 18230165 · PMC2248577 · Lipids in health and disease · 2008 · 8 claims · 8 setups

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Serum depletion induces calcification (mineral Ca/P deposition) in rabbit aortic smooth muscle cell culture

rabbit calcifying alizarin fourier-transform dose-response
Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes.

PMID 19833877 · PMC2797941 · Diabetes · 2010 · 7 claims · 5 setups

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Mitochondrial protein abundance is decreased in insulin-resistant (obese and type 2 diabetic) skeletal muscle

skeletal volunteers bsa shotgun euglycemic-hyperinsulinemic immunoblot
A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.

PMID 39108562 · PMC11301579 · Ecology and evolution · 2024 · 7 claims · 2 setups

Has reproduction · 93

624 DEGs were identified between summer (M7) and fall (M10) migratory P. flavescens, with 352 upregulated and 272 downregulated in M7 versus M10

pantala bulk qrt-pcr
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls

activated skeletal muscle altered affymetrix quantitative sirna
Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

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Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

liver atherosclerotic 128-gene independent two-way gene bioinformatic
With the finished human genome in hand, what next?

PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

domestic saccharomyces systemic schistosoma comparative functional genetic
Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar).

PMID 33158415 · PMC7648306 · Genetics, selection, evolution : GSE · 2020 · 7 claims · 5 setups

Has reproduction · 85

A QTL for pre-smolt growth was identified on chromosome 9.

atlantic isotope snp rnaseq
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

lms independent soft gene array immunohistochemistry
Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

Has reproduction · 73

N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence
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
Endurance exercise as a countermeasure for aging.

PMID 18716044 · PMC2570389 · Diabetes · 2008 · 8 claims · 8 setups

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Reduced insulin sensitivity with age is likely related to adiposity and physical inactivity rather than being an inevitable consequence of aging.

vastus mitochondria mitochondrial extracted euglycemic-hyperinsulinemic mitochondrial citrate
Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

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A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

lsl-krasg12d soft combined mfh microarray gene oncogenic
Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

PMID 33722289 · PMC7962346 · Genome biology · 2021 · 6 claims · 7 setups

Has reproduction · 66

A PE2-mediated single-base (C>G) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder but not heart or brain, mirroring HDR-mediated 3-bp substitution.

zygotes aorta genomic aortae crispr prime quantitative
Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

PMID 40211845 · PMC12229932 · Animal bioscience · 2025 · 7 claims · 5 setups

Has reproduction · 71

311 SNPs and 73 candidate genes (e.g., IGF2BP1, BMP3, ACSL5) are significantly associated with carcass traits in Sanhuang chickens

sanhuang chickens chicken breast whole-genome phenotypic genomic
Analysis of human sarcospan as a candidate gene for CFEOM1.

PMID 11180757 · PMC29083 · BMC genetics · 2001 · 7 claims · 5 setups

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Sarcospan sequence is unmutated in all six CFEOM1 families studied

yac genomic extraocular genome pcr direct immunofluorescence
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

bovine pcr-based comparative rt-pcr
MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups

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High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status

high ovarian mir-29a mirna unsupervised significance
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.

PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 7 setups

Has reproduction · 97

TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.

aortic brown genes training wgcna biological gsva

Experiments

Induction of calcification by serum depletion in cell culture: a model for focal calcification in aortas related to atherosclerosis.

Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes.

A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

With the finished human genome in hand, what next?

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar).

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

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

Endurance exercise as a countermeasure for aging.

Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

Analysis of human sarcospan as a candidate gene for CFEOM1.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.