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 10

System / cell line: cns ✕ Assay: gene-expression ✕ Clear

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

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Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

normal genome-wide same omim microarray sage computational
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
Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.

PMID 41857393 · PMC13061643 · Nature neuroscience · 2026 · 8 claims · 6 setups

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Adult spinal-cord-derived human oligodendroglia and astrocytes, but not microglia, show primed chromatin signatures at HOX loci and a putative SOX10 enhancer.

postmortem induced lentiviral cns single-nucleus nanocut&tag high-resolution
The identification of a Distinct Astrocyte Subtype that Diminishes in Alzheimer's Disease.

PMID 38502590 · PMC11567244 · Aging and disease · 2024 · 7 claims · 7 setups

Has reproduction · 57

A distinct astrocyte subpopulation marked by low GFAP, AQP4+, and CD63+ expression exists in normal brain and is functionally enriched for Aβ clearance and tau protein binding

hippocampus prefrontal astrocyte frontal single-nuclei gene cell-cell
Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

Has reproduction · 26

The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

acutely microglia c57bl meta-analysis integration spectral
Systems biology approaches for the study of multiple sclerosis.

PMID 18505469 · PMC3865652 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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The MHC locus on chromosome 6p21 is the strongest genetic region linked to MS susceptibility.

patients lesion osteopontin monocyte-depleted genetic large-scale gene
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
Developmental stage dominates cell-type identity and reveals a chromatin regulatory function for Rad50 in Drosophila.

PMID 41978263 · PMC13076223 · Nucleic acids research · 2026 · 8 claims · 8 setups

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Developmental stage is a stronger determinant of transcriptional identity than cell type across Drosophila neurons, glia, and hemocytes

neurons cns e16 salivary bulk atac-seq western
Stemming cancer: functional genomics of cancer stem cells in solid tumors.

PMID 18561035 · PMC2758383 · Stem cell reviews · 2008 · 8 claims · 8 setups

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Cancer stem cells are a minority tumor subpopulation that alone can maintain indefinite tumor growth, as shown by serial transplantation experiments

solid fetal cd133+ breast facs neurosphere genome-wide
Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.

PMID 42010620 · PMC13227897 · Journal of neuroinflammation · 2026 · 8 claims · 5 setups

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Morphine-dependent macaques show increased CD4+ TCM and Treg cell proportions and decreased CD8+ TEM cell proportions in CSF at the pre-infection timepoint compared to saline controls

csf scrna-seq necropsy single-cell flow cell-cell

Experiments

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

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

Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.

The identification of a Distinct Astrocyte Subtype that Diminishes in Alzheimer's Disease.

Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

Systems biology approaches for the study of multiple sclerosis.

Neuroscience in the era of functional genomics and systems biology.

Developmental stage dominates cell-type identity and reveals a chromatin regulatory function for Rad50 in Drosophila.

Stemming cancer: functional genomics of cancer stem cells in solid tumors.

Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.