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Links from GEO DataSets

Items: 20

1.

The effect of HDAC inhibitor, 4b, on skeletal muscle gene expression

(Submitter supplied) To assess the effects of histone deacetylase (HDAC) inhibitor, HDACi 4b, treatment on muscle function on a molecular level, we performed microarray analysis on skeletal muscle (gastrocnemius) samples from wt and N17182Q mice treated with the HDAC inhibitor 4b for 3 months (50 mg/kg; s.c. injection 3x weekly; n=4 per group). The transcriptome pattern in N17182Q mice compared to wt controls consisted of deficits in the expression of genes related to mitochondrial function and oxidative metabolism. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
16 Samples
Download data: TXT
Series
Accession:
GSE56963
ID:
200056963
2.

HDAC inhibition imparts beneficial transgenerational effects in Huntington's disease mice via altered DNA and histone methylation

(Submitter supplied) Increasing evidence has demonstrated that epigenetic factors can profoundly influence gene expression and, in turn, influence resistance or susceptibility to disease. Epigenetic drugs, such as histone deacetylase (HDAC) inhibitors, are finding their way into clinical practice, although their exact mechanisms of action are unclear. To identify mechanisms associated with HDAC inhibition, we performed microarray analysis on brain and muscle samples treated with the HDAC1/3-targeting inhibitor, HDACi 4b. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
12 Samples
Download data: IDAT, TXT
Series
Accession:
GSE67733
ID:
200067733
3.

The HDAC inhibitor 4b ameliorates the disease phenotype and transcriptional abnormalities in Huntington's disease transgenic mice

(Submitter supplied) Transcriptional dysregulation has emerged as a core pathologic feature of Huntington's disease (HD), one of several triplet-repeat disorders characterized by movement deficits and cognitive dysfunction. Although the mechanisms contributing to the gene expression deficits remain unknown, therapeutic strategies have aimed to improve transcriptional output via modulation of chromatin structure. Recent studies have demonstrated therapeutic effects of commercially available histone deacetylase (HDAC) inhibitors in several HD models; however, the therapeutic value of these compounds is limited by their toxic effects. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6103
47 Samples
Download data: CSV
Series
Accession:
GSE26317
ID:
200026317
4.

Histones associated with downregulated genes are hypo-acetylated in Huntington’s disease models

(Submitter supplied) Transcriptional dysregulation plays a major role in the pathology of Huntington's disease (HD). However, the mechanisms causing selective downregulation of genes remain unknown. Histones regulate chromatin structure and thereby control gene expression; recent studies have demonstrated a therapeutic role for histone deacetylase (HDAC) inhibitors in polyglutamine diseases. This study demonstrates that despite no change in overall acetylated histone levels, histone H3 is hypo-acetylated at promoters of downregulated genes in R6/2 mice, ST14a and STHdh cells, as demonstrated by in vivo chromatin immunoprecipitation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
8 Samples
Download data: CEL, CHP
Series
Accession:
GSE11358
ID:
200011358
5.

Alterations in Sperm DNA Methylation, Non-coding RNA and Histone Retention Associate with DDT Induced Epigenetic Transgenerational Inheritance of Disease

(Submitter supplied) Environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease through the germline. This study was designed to investigate DDT induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to DDT during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed.
Organism:
Rattus norvegicus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL18694
30 Samples
Download data: CSV
Series
Accession:
GSE109775
ID:
200109775
6.

Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites

(Submitter supplied) Female and male rats of an outbred female Sprague Dawley rats were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), or DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). Treatment lineages are designated “control” or “vinclozolin” or “DDT” lineages. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. more...
Organism:
Rattus norvegicus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18694
23 Samples
Download data: CSV
Series
Accession:
GSE106125
ID:
200106125
7.

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL16570
15 Samples
Download data: CEL
Series
Accession:
GSE66052
ID:
200066052
8.

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally [embryo]

(Submitter supplied) A father’s lifetime experiences can be transmitted to his offspring to affect health and development. The mechanisms underlying paternal epigenetic transmission are unclear. Unlike somatic cells, there are few nucleosomes in sperm and their function in epigenetic inheritance is unknown. We generated transgenic mice in which overexpression of the histone H3 lysine 4 (H3K4) demethylase LSD1/KDM1A during spermatogenesis reduced H3K4 dimethylation in sperm. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL16570
8 Samples
Download data: CEL
Series
Accession:
GSE66051
ID:
200066051
9.

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally [sperm]

(Submitter supplied) A father’s lifetime experiences can be transmitted to his offspring to affect health and development. The mechanisms underlying paternal epigenetic transmission are unclear. Unlike somatic cells, there are few nucleosomes in sperm and their function in epigenetic inheritance is unknown. We generated transgenic mice in which overexpression of the histone H3 lysine 4 (H3K4) demethylase LSD1/KDM1A during spermatogenesis reduced H3K4 dimethylation in sperm. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL16570
7 Samples
Download data: CEL
Series
Accession:
GSE66050
ID:
200066050
10.

Proper chromatin programming during spermatogenesis is required for embryonic development

(Submitter supplied) Epigenetic mechanisms including DNA methylation, non-coding RNAs and histone modifications control gene expression. Studies suggest that a father's lifetime experiences can be transmitted to his offspring to affect development and health. The mechanisms underlying such epigenetic inheritance are unknown. A potential route for paternal transmission is the unique chromatin composition of spermatozoa. Unlike somatic cells and oocytes, most nucleosomes in sperm are replaced with protamine nucleoproteins. The role of residual nucleosomes, residing at gene regulatory sequences, for epigenetic control of embryonic development is unknown. Here we generated a transgenic mouse model in which over-expression of the histone H3 lysine 4 (H3K4) demethylase LSD1/KDM1A during spermatogenesis alters H3K4 methylation in sperm. Strikingly, KDM1A over-expression in one generation causes severe embryonic defects in non-transgenic descendants spanning three subsequent generations. We show for the first time that correct histone methylation homeostasis during spermatogenesis is critical for offspring development and survival over multiple generations.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
7 Samples
Download data: WIG
Series
Accession:
GSE55471
ID:
200055471
11.

Epigenome-Wide Association Study for Atrazine Induced Transgenerational Histone Retention Sperm Epigenetic Biomarkers for Disease

(Submitter supplied) Atrazine is a common agricultural herbicide previously shown to promote epigenetic transgenerational inheritance of disease to subsequent generations. The current study was designed as an epigenome-wide association study (EWAS) to identify transgenerational sperm disease associated differential histone retention regions (DHRs). Gestating female F0 generation rats were transiently exposed to atrazine during the period of embryonic gonadal sex determination, and then subsequent F1, F2, and F3 generations obtained in the absence of any continued exposure. more...
Organism:
Rattus norvegicus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18694
67 Samples
Download data: CSV
Series
Accession:
GSE156530
ID:
200156530
12.

DNA methylation profiling in human Huntington's Disease brain

(Submitter supplied) Despite extensive progress in Huntington’s Disease (HD) research, very little is known about the association of epigenetic variation and HD pathogenesis in human brain tissues. Moreover, its contribution to the tissue-specific transcriptional regulation of the huntingtin gene (HTT), in which HTT expression levels are highest in brain and testes, is currently unknown. To investigate the role of DNA methylation in HD pathogenesis and tissue-specific expression of HTT, we utilized the Illumina HumanMethylation450K BeadChip array to measure DNA methylation in a cohort of age-matched HD and control human cortex and liver tissues. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
18 Samples
Download data: CSV, IDAT
Series
Accession:
GSE79064
ID:
200079064
13.

Effect of high fat diet versus low fat diet on histone distribution in sperm of male mice

(Submitter supplied) Several studies have described phenotypic changes in offspring of mice exposed to environmental factors including diet, but the effect of diet on sperm chromatin remains unclear. We used a high fat diet (HFD) induced obesity mouse model, and examined chromatin of paternal spermatozoa. We performed chromatin immunoprecipitation followed by high throughput sequencing using specific H3 antibodies or specific H3K4me1antibodies.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
10 Samples
Download data: WIG
Series
Accession:
GSE72211
ID:
200072211
14.

Human blood expression for Huntington's disease versus control, Codelink

(Submitter supplied) Codelink Human Uniset I, II, and 20K expression levels for 12 symptomatic and 5 presymptomatic Huntington's disease patients versus 14 healthy controls. Keywords: other
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS1332
Platform:
GPL1449
31 Samples
Download data
Series
Accession:
GSE1767
ID:
200001767
15.

Human blood expression for Huntington's disease versus control

(Submitter supplied) Affymetrix U133A expression levels for 12 symptomatic and 5 presymptomatic Huntington's disease patients versus 14 healthy controls. Keywords: other
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS1331
Platform:
GPL96
31 Samples
Download data
Series
Accession:
GSE1751
ID:
200001751
16.
Full record GDS1332

Huntington's disease: peripheral blood expression profile (Codelink Uniset 20K)

Analysis of blood samples of 5 presymptomatic and 12 symptomatic Huntington's disease (HD) patients. Studies suggest that gene expression may be altered in a variety of tissues in HD, including peripheral blood. Results identify potential markers for HD.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 3 disease state sets
Platform:
GPL1449
Series:
GSE1767
31 Samples
Download data
17.
Full record GDS1331

Huntington's disease: peripheral blood expression profile (HG-U133A)

Analysis of blood samples of 5 presymptomatic and 12 symptomatic Huntington's disease (HD) patients. Studies suggest that gene expression may be altered in a variety of tissues in HD, including peripheral blood. Results identify potential markers for HD.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 3 disease state sets
Platform:
GPL96
Series:
GSE1751
31 Samples
Download data
18.

Integrative DNA methylation and gene expression analyses identify DNA packaging and epigenetic regulatory genes associated with low motility sperm

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by array
Platforms:
GPL8490 GPL6244
39 Samples
Download data: CEL, CHP
Series
Accession:
GSE26982
ID:
200026982
19.

Sperm DNA methylation

(Submitter supplied) BACKGROUND: In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. METHODS AND RESULTS: Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL8490
21 Samples
Download data: TXT
Series
Accession:
GSE26974
ID:
200026974
20.

mRNA Content of Human Sperm

(Submitter supplied) BACKGROUND: In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. METHODS AND RESULTS: Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
18 Samples
Download data: CEL, CHP
Series
Accession:
GSE26881
ID:
200026881
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