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).
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Insights into the physiology of childbirth using transcriptomics.
PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups
Labor results in a change in the transcriptome in each component of the uterus studied
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Quantitative phosphoproteomics by mass spectrometry: past, present, and future.
PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups
Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS
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Has reproduction · 81
Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer.
PMID 33777753 · PMC7991912 · Frontiers in oncology · 2021 · 7 claims · 8 setups
Cisplatin exposure induces significant deregulation of protein expression networks in NSCLC cells
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Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.
PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups
DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue
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Quantitative mass spectrometry of diabetic kidney tubules identifies GRAP as a novel regulator of TGF-beta signaling.
PMID 19836472 · PMC2829334 · Biochimica et biophysica acta · 2010 · 8 claims · 7 setups
Label-free 2D-LC-MS/MS quantitative proteomics identified 476 significantly differentially expressed proteins in kidney tubules of diabetic OVE26 mice versus control mice
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Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.
PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups
Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation
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Has reproduction · 81
Transcriptome analysis reveals differential splicing events in IPF lung tissue.
PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups
873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.
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Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.
PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups
QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker
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Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.
PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups
Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid
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Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.
PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups
Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung
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Has reproduction · 10
Effect of PAIP1 on the metastatic potential and prognostic significance in oral squamous cell carcinoma.
PMID 35153296 · PMC8841500 · International journal of oral science · 2022 · 8 claims · 8 setups
PAIP1 mRNA and protein levels are upregulated in OSCC/HNSCC compared to normal tissue.
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Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.
PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups
CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.
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Has reproduction
Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).
PMID 41745774 · PMC12945099 · Toxins · 2026 · 8 claims · 4 setups
This is the first characterization of the venom profiles (transcriptomic and proteomic) of the genus Coniophanes.
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Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways.
PMID 16001973 · PMC1183194 · BMC cancer · 2005 · 6 claims · 5 setups
The number of significantly differentially expressed probesets induced by each drug correlates with the known clinical therapeutic response rate of that drug in fibrosarcoma
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Genomic and proteomic profiling II: comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars.
PMID 17718906 · PMC2039739 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 4 setups
1124 transcripts (1103 genes; 732 over-expressed, 371 under-expressed) are differentially expressed in leiomyomas compared to keloids/incisional scars
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Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.
PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups
125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells
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Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.
PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups
aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases
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Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.
PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups
151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations
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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
Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls
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Genetics and functional genomics of type 2 diabetes mellitus.
PMID 14659011 · PMC329413 · Genome biology · 2003 · 7 claims · 5 setups
Genome-wide transcription profiling of diabetic skeletal muscle reveals coordinated downregulation of oxidative phosphorylation genes, converging on PGC1α as a central regulator.