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).

• Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.

  PMID 19893615 · PMC2764086 · PloS one · 2009 · 8 claims · 8 setups

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  Simultaneous analysis of 347 thyroid samples across 12 histological classes from six datasets improves definition of diagnostic markers compared to prior binary-class studies

  thyroid microarray gene real-time

• Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

  PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups

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  Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1

  surgical standardized glioma gbm western principal k-means

• A large-scale proteomic analysis of human embryonic stem cells.

  PMID 18162134 · PMC2211323 · BMC genomics · 2007 · 8 claims · 5 setups

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  Two large-scale western blot systems (PowerBlot, Kinexus) identify over 600 proteins expressed in undifferentiated hESCs across 18 functional classes

  bg01 bg03 hescs powerblot kinexus immunofluorescence

• CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

  PMID 16995941 · PMC1592126 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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  CROPPER is a web-based software resource that combines genomic data from heterogeneous sources using identifier and orthologous gene information from the Ensembl database.

  mus substantia transgenic mptp-lesioned western microarray self-organizing

• 93rd Annual Meeting of the American Association for Cancer Research, San Francisco, CA, USA, 6-10 April 2002.

  PMID 12100742 · PMC138737 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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  Serial analysis of gene expression identifies genes preferentially expressed in ductal carcinoma in situ

  breast laser serum bladder cdna western seldi-tof

• Thermogenic adipocytes promote HDL turnover and reverse cholesterol transport.

  PMID 28422089 · PMC5399294 · Nature communications · 2017 · 8 claims · 8 setups

  Has reproduction

  Pharmacological (CL316,243) activation of thermogenic adipocytes increases HDL-cholesterol and reduces atherosclerosis in E3L.CETP mice, with HDL-cholesterol an independent predictor of atherosclerosis

  c57bl hdl plasma peritoneal fplc lipidomics cholesterol

• The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

  PMID 30899024 · PMC6428865 · Nature communications · 2019 · 7 claims · 8 setups

  Has reproduction · 85

  Xrn1 promotes translation of a specific group of mRNAs encoding membrane/secretome proteins, acting at translation initiation.

  cerevisiae yeast xrn1∆ western luciferase polysome

• Genomic and proteomic profiling of responses to toxic metals in human lung cells.

  PMID 12760830 · PMC1241504 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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  Toxic metals (Cd, Cr, Ni, As) each induce a largely distinct, metal-specific pattern of gene expression changes in BEAS-2B human bronchial epithelial cells

  beas-2b cdna western kinetworks

• Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

  PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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  MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

  prostate subset lncap 22rv1 microrna quantitative western

• Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity.

  PMID 40846763 · PMC12425804 · Nature genetics · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  BRG1 chromatin binding decreases linearly and proportionally with BRG1 protein dosage, independent of TFs or histone modifications (92.2% of binding peaks follow a linear model).

  brg1-fkbp12-f36v brg1-knock-in snf2h-fkbp12-f36v mes western cut&run atac-seq

• Exosomal microRNA miR-92a concentration in serum reflects human brown fat activity.

  PMID 27117818 · PMC4853423 · Nature communications · 2016 · 8 claims · 8 setups

  Has reproduction · 97

  Brown and beige adipocytes release exosomes, and thermogenic activation increases exosome release both in vitro and in vivo.

  brown tissues serum exosomes electron exosome mirna

• Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

  PMID 26969729 · PMC4812528 · Molecular systems biology · 2016 · 7 claims · 6 setups

  Has reproduction · 67

  Cell adhesion (cell-cell and cell-ECM) pathways are significantly and consistently dysregulated in women who develop familial breast cancer across multiple omic data types and tissues.

  peripheral pbmcs normal snap-frozen gene exome western

• Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.

  PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 8 claims · 8 setups

  Has reproduction · 73

  NF1 is highly expressed in cetuximab-sensitive CRC cell lines and minimally expressed in cetuximab-resistant ones

  crc cetuximab-sensitive sirna ffpe western growth colony

• Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

  PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

  heart degs dgat2 mitodegs microarray kegg protein-protein

• What defines a photosynthetic microbial mat in western Antarctica?

  PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions

  microbial quality-filtered overflowing shotgun taxonomic alpha

• Pathway analysis of kidney cancer using proteomics and metabolic profiling.

  PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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  31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

  ccrcc rcc computational random gel immunoblotting immunohistochemistry

• Genomic and proteomic profiling I: leiomyomas in African Americans and Caucasians.

  PMID 17716379 · PMC2063502 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 6 setups

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  268 genes (177 over-expressed, 91 under-expressed) are differentially expressed in leiomyomas of African Americans compared to Caucasians (P<0.01, 2-fold cutoff)

  paired same excised paraffin-embedded microarray realtime 2d-page

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Characterization of the placental macrophage secretome: implications for antiviral activity.

  PMID 19070362 · PMC2947718 · Placenta · 2009 · 7 claims · 5 setups

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  PM and MDM secrete different soluble proteins, some of which may contribute to decreased HIV-1 replication in PM

  placental seldi-tof sds-page western

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr