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).

• Molecular tumor profiling: translating genomic insights into clinical advances.

  PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

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  Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

  breast ovarian panel tumor gene-expression candidate-gene large-scale

• Spinocerebellar ataxia type 23: a genetic update.

  PMID 19089525 · PMC2694919 · Cerebellum (London, England) · 2009 · 8 claims · 6 setups

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  The SCA23 disease locus maps to chromosome 20p13-12.3, spanning ~6 Mb and containing 97 known/predicted genes.

  members post-mortem candidate coding genome-wide neuropathological southern

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• Divide and conquer: progress in the molecular stratification of cancer.

  PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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  Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

  breast nsclc colon early-stage immunohistochemistry gene comparative

• Application of functional genomics to primate endometrium: insights into biological processes.

  PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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  Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

  endometrial uterus whole-genome cdna oligonucleotide

• Alcohol consumption and breast tumor mitochondrial DNA mutations.

  PMID 19847642 · PMC4403627 · Breast cancer research and treatment · 2010 · 8 claims · 6 setups

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  Somatic mtDNA mutations are a frequent occurrence in breast tumors

  breast paraffin-embedded blood study ttge sequencing immunohistochemistry

• Advances in breast cancer: pathways to personalized medicine.

  PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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  Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

  population-based women breast high-risk germline genome-wide microarray

• Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.

  PMID 32959884 · PMC7689298 · Human molecular genetics · 2020 · 8 claims · 8 setups

  Has reproduction · 67

  Trem2 R47H knock-in mice show gene dose-dependent decreased Trem2 expression in hippocampus, largely due to altered splicing

  hippocampal microglia conditioned rt-qpcr immunohistochemistry glial

• Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

  PMID 33086062 · PMC7649750 · Cell reports · 2020 · 8 claims · 8 setups

  Has reproduction · 59

  KMT2D is a potent tumor suppressor in melanoma

  hmel-brafv600e tyr-creert2 tma kmt2d pooled xenograft genetically

• Genomic and epigenetic instability in colorectal cancer pathogenesis.

  PMID 18773902 · PMC2866182 · Gastroenterology · 2008 · 8 claims · 7 setups

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  Genomic instability (CIN or MSI) is a key early molecular step in colorectal tumorigenesis that may initiate rather than merely accompany the adenoma-carcinoma sequence

  colon embryonic colorectal inter immunohistochemistry karyotype

• Development of a fluorescent multiplex assay for detection of MSI-High tumors.

  PMID 15528789 · PMC3839403 · Disease markers · 2004 · 8 claims · 7 setups

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  Mononucleotide markers are the most sensitive and specific microsatellite marker type for detecting MSI-H tumors with MMR defects

  colorectal blood healthy non-msi-h microsatellite fluorescent immunohistochemistry

• Neurofibrillary tau pathology modulated by genetic variation of alpha-synuclein.

  PMID 18661559 · PMC8957216 · Annals of neurology · 2008 · 7 claims · 5 setups

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  The SNCA intron 4 marker rs2572324 is associated with the extent of neurofibrillary tangle (Braak stage) pathology.

  postmortem whole-genome-amplified vantaa85+ neuropathological immunohistochemistry snp

• Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

  PMID 19943934 · PMC2794290 · BMC cancer · 2009 · 8 claims · 5 setups

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  Hundreds of genes differentiate GISTs according to KIT versus PDGFRA mutation and expression status, despite no discriminative profile for clinical/pathological parameters.

  frozen genomic formalin-fixed differentially microarray sequencing quantitative

• The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

  PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups

  Has reproduction · 67

  A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.

  facs-isolated fcrls+ sorted app-ps1 nanostring sequencing quantitative

• Role of FGFR3 in urothelial cell carcinoma: biomarker and potential therapeutic target.

  PMID 17912529 · PMC4876910 · World journal of urology · 2007 · 8 claims · 8 setups

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  Activating FGFR3 mutations occur frequently in bladder cancer and are strongly associated with low tumour grade and stage

  bladder normal urothelial mutation allele-specific laser

• Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

  PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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  Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

  serous same lmp braf-mutant gene hotspot erbb2

• Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

  PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 76

  DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples

  fresh matched archived dsrct scrna-seq single-nucleus bulk

• Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

  PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes

  melanogaster dgrp drosophila genes bulk locomotor gene