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ProteomicsA Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules
Cells expressing mutant huntingtin were treated in triplicate with serum-free DMEM with vehicle (Q111SST) or serum-free DMEM with one of 4 protective compounds (Cyproheptadine, Loxapine, Diacylglycerol Kinase Inhibitor II, Meclizine) for 24 hours. Wild type cells were also treated with serum-free DM...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2019-11-20 | MSV000084607 | MassIVE
TranscriptomicsA quantitative model of transcription regulation reveals the role of non-conserved enhancers
We identify sites of combinatorial control by performing high throughput ChIP experiments on p300, CREB-binding protein (CBP), the deacetylase SIRT1 and on multiple DNA-binding transcription factors in three different tissues. We present a quantitative model of transcriptional regulation that revea...
ORGANISM(S): Mus musculus 
2010-05-12 | E-GEOD-17067 | biostudies-arrayexpress
GenomicsGenome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes
We use ChIP-seq to discover the genome-wide sites of acetylation of lysine 56 of the histone H3 (H3K56), which is a target of three histone modifying enzymes with known roles in diabetes and insulin resistance, in human adipocytes derived from mesenchymal stem cells. Surprisingly, we find that a ver...
ORGANISM(S): Homo sapiens 
2011-05-31 | E-GEOD-24326 | biostudies-arrayexpress
GenomicsExtensive changes in DNA methylation are associated with expression of mutant huntingtin [ChIP-seq]
The earliest stages of HuntingtonM-bM-^@M-^Ys disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin protein (HTT). To explore the hypothesis DNA methylation may be altered in cells expressing mutate...
ORGANISM(S): Mus musculus 
2013-01-24 | E-GEOD-43429 | biostudies-arrayexpress
TranscriptomicsExtensive changes in DNA methylation are associated with expression of mutant huntingtin [mRNA-seq]
The earliest stages of Huntington’s disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin protein (HTT). To explore the hypothesis DNA methylation may be altered in cells expressing mutated HTT, we ...
ORGANISM(S): Mus musculus 
2013-01-24 | E-GEOD-43431 | biostudies-arrayexpress
GenomicsExtensive changes in DNA methylation are associated with expression of mutant huntingtin [RRBS]
The earliest stages of Huntington’s disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin protein (HTT). To explore the hypothesis DNA methylation may be altered in cells expressing mutated HTT, we ...
ORGANISM(S): Mus musculus 
2013-01-24 | E-GEOD-43432 | biostudies-arrayexpress
GenomicsExtensive changes in DNA methylation are associated with expression of mutant huntingtin [MeDIP-seq]
The earliest stages of Huntington’s disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin protein (HTT). To explore the hypothesis DNA methylation may be altered in cells expressing mutated HTT, we ...
ORGANISM(S): Mus musculus 
2013-01-24 | E-GEOD-43430 | biostudies-arrayexpress
GenomicsUnbiased, Genome-wide in vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-specific Liver Gene Expression
We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation and diseas...
ORGANISM(S): Mus musculus 
2010-09-28 | E-GEOD-21777 | biostudies-arrayexpress
ProteomicsProteomics, post-translational modifications, and integrative analyses reveal heterogeneity of molecular mechanisms within medulloblastoma subgroups
Archer TC, Ehrenberger T, Mundt F, Gold MP, Krug K, Mah CK, Mahoney EL, Daniel CJ, LeNail A, Ramamoorthy D, Mertins P, Mani DR, Zhang H, Gillette MA, Clauser K, Noble M, Tang LC, Francois JP, Silterra J, Jensen J, Tamayo P, Korshunov A, Pfister SM, Kool M, Northcott PA, Sears RC, Lipton JO, Carr SA,...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-07-20 | MSV000082644 | MassIVE
TranscriptomicsPolyglutamine expanded huntingtin dramatically alters the genome-wide binding of HSF1 (mRNA)
In Huntington's disease (HD), polyglutamine expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation of the heat shock response can reduce many of the effects of mutant Htt in d...
ORGANISM(S): Mus musculus 
2012-06-18 | E-GEOD-38001 | biostudies-arrayexpress
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