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: brain ✕ Assay: stem ✕ Clear

GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

PMID 16919418 · PMC2842930 · Genomics · 2006 · 8 claims · 8 setups

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Human FXN YAC transgenes containing GAA repeat expansions (YG22, YG8) rescue the embryonic lethality of homozygous Fxn knockout mice

yg22 tissues lysates sciatic breeding semiquantitative 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
Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.

PMID 41345108 · PMC12789597 · Nature communications · 2025 · 7 claims · 8 setups

Has reproduction · 93

SIRT6 is an evolutionarily conserved regulator of tryptophan catabolism that balances tryptophan usage between the kynurenine and serotonin/melatonin pathways

embryonic brains sirt6 serum untargeted rna-seq microarray
Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

Has reproduction · 95

Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

embryonic escs dem-cgis demg methylation chip-seq gene
Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

pediatric same oligonucleotide quantitative
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.

PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups

Has reproduction · 78

TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.

embryonic trim28 mrna-seq trim28 h3k9me3
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
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
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular

Experiments

GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

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

Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.

Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.

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

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

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.