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).

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

  PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

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  Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

  alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 75

  All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.

  haβ-ki models degs app bulk functional master

• Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

  PMID 18922787 · PMC3523710 · Science signaling · 2008 · 8 claims · 8 setups

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  VILIP1 was identified via a proteomic (GST pull-down) approach as a protein interacting with the P2X2 receptor C-terminal tail

  brain hek gst co-immunoprecipitation immunocytochemistry

• Alzheimer's disease biomarker discovery in symptomatic and asymptomatic patients: experimental approaches and future clinical applications.

  PMID 19796674 · PMC2840994 · Experimental gerontology · 2010 · 8 claims · 4 setups

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  cDNA microarray screening of 6794 genes identified 32 genes aberrantly expressed (>1.8-fold) in the superior temporal gyrus of moderate dementia cases versus cognitively normal controls

  post-mortem cortico-hippocampal cdna western culture

• The FAS gene, brain volume, and disease progression in Alzheimer's disease.

  PMID 19766542 · PMC3100774 · Alzheimer's & dementia : the journal of the Alzheimer's Association · 2010 · 8 claims · 4 setups

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  The minor (T) allele of rs1468063 in FAS is significantly associated with faster AD progression after permutation-based multiple-testing correction

  peripheral longitudinally same subset snp survival permutation

• Genomic studies of mood disorders -- the brain as a muscle?

  PMID 15833130 · PMC1088952 · Genome biology · 2005 · 7 claims · 5 setups

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  FGF family members and receptors (notably FGF1, FGF2, FGFR2, FGFR3) are down-regulated in postmortem prefrontal cortex of subjects with major depressive disorder but not in bipolar or control subjects.

  postmortem brain rodent hippocampus affymetrix quantification gene

• Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

  PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity

  peripheral hippocampal spinal peritumoral microarray protein-protein

• Neuroplasticity, psychosocial genomics, and the biopsychosocial paradigm in the 21st century.

  PMID 19728478 · PMC2933650 · Health & social work · 2009 · 8 claims · 8 setups

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  Recent neuroplasticity and psychosocial genomics research validates and elaborates Engel's biopsychosocial paradigm by revealing mechanisms linking psychosocial experience to neurobiology.

  experienced long-term ocd women structural eeg attentional

• In vivo prime editing rescues alternating hemiplegia of childhood in mice.

  PMID 40695277 · PMC12702498 · Cell · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  PE and BE strategies efficiently correct five prevalent ATP1A3 mutations (D801N, E815K, L839P, G947R-A, G947R-C) in HEK293T cells and AHC patient-derived iPSCs, with 43%-90% correction in iPSCs.

  hek293t ahc n2a b6c3.atp1a3 prime circle-seq rhampseq

• Expanding the vision of environmental health at UNC-CH.

  PMID 15248304 · PMC1247395 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  Human breast tumors arise from at least two distinct cell types, basal and luminal epithelial, with different clinical behavior

  breast chinese carolina rodent microarray functional genetic