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Links from GEO DataSets

Items: 20

1.

Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome (Hi-C)

(Submitter supplied) Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that HGPS cells experience genome-wide alterations in patterns of H3K27me3 deposition, changes in the associations of genomic loci with nuclear lamin A/C, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains that characterizes chromosome folding in normal cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9115
4 Samples
Download data: TXT
Series
Accession:
GSE41763
ID:
200041763
2.

Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9115 GPL9052 GPL570
28 Samples
Download data: BED, CEL, TXT
Series
Accession:
GSE41764
ID:
200041764
3.

Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome (ChIP-seq)

(Submitter supplied) Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that HGPS cells experience genome-wide alterations in patterns of H3K27me3 deposition, changes in the associations of genomic loci with nuclear lamin A/C, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains that characterizes chromosome folding in normal cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9052
18 Samples
Download data: BED
Series
Accession:
GSE41757
ID:
200041757
4.

Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome (expression)

(Submitter supplied) Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that HGPS cells experience genome-wide alterations in patterns of H3K27me3 deposition, changes in the associations of genomic loci with nuclear lamin A/C, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains that characterizes chromosome folding in normal cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
6 Samples
Download data: CEL
Series
Accession:
GSE41751
ID:
200041751
5.

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20301 GPL11154
17 Samples
Download data
Series
Accession:
GSE150138
ID:
200150138
6.

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome (RNA-Seq)

(Submitter supplied) Hutchinson-Gilford Progeria Syndrome (HGPS) is a progeroid disease characterized by the early onset of some classically age-related phenotypes including arthritis, loss of body fat and hair and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein Lamin A (termed Progerin) and have previously been shown to exhibit prominent chromatin changes. Here, we identify epigenetic deregulation of lamina-associated domains (LADs) as a central feature in the molecular pathology of HGPS. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
9 Samples
Download data: TXT
7.

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome (ATAC-Seq)

(Submitter supplied) Hutchinson-Gilford Progeria Syndrome (HGPS) is a progeroid disease characterized by the early onset of some classically age-related phenotypes including arthritis, loss of body fat and hair and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein Lamin A (termed Progerin) and have previously been shown to exhibit prominent chromatin changes. Here, we identify epigenetic deregulation of lamina-associated domains (LADs) as a central feature in the molecular pathology of HGPS. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
8 Samples
Download data: XLS
Series
Accession:
GSE150136
ID:
200150136
8.

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome

(Submitter supplied) Hutchinson-Gilford Progeria Syndrome (HGPS) is a progeroid disease characterized by the early onset of some classically age-related phenotypes including arthritis, loss of body fat and hair and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein Lamin A (termed Progerin) and have previously been shown to exhibit prominent chromatin changes. Here, we identify epigenetic deregulation of lamina-associated domains (LADs) as a central feature in the molecular pathology of HGPS. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL23976
15 Samples
Download data: IDAT
Series
Accession:
GSE149960
ID:
200149960
9.

Reprogramming Hutchinson-Gilford Progeria Syndrome fibroblasts resets epigenomic landscape in patient-derived induced pluripotent stem cells [ChIP-Seq]

(Submitter supplied) Hutchinson-Gilford Progeria Syndrome (HGPS) is a segmental premature aging disorder caused by the accumulation of the truncated form of Lamin A known as Progerin within the nuclear lamina. Cellular hallmarks of HGPS include nuclear blebbing, loss of peripheral heterochromatin, defective epigenetic inheritance, altered gene expression, and senescence. To model HGPS using iPSCs, detailed genome-wide and structural analysis of the epigenetic landscape is required to assess the initiation and progression of the disease.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10999
16 Samples
Download data: BED, TXT
Series
Accession:
GSE84356
ID:
200084356
10.

SAMMY-seq, H3K9me3 and H3K27me3 ChIP-seq and RNA-seq of control and progeria fibroblasts

(Submitter supplied) We present a new high-throughput sequencing-based technique, named Sequential Analysis of MacroMolecules accessibilitY (SAMMY-seq), for the genome-wide mapping of chromatin regions separated by differential accessibility. The method is based on the sequential extraction of multiple chromatin fractions, corresponding to increasingly compacted and less accessible chromatin regions, which are mapped along the genome using high-throughput sequencing. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms:
GPL16791 GPL24676 GPL11154
76 Samples
Download data: BED, BIGWIG, BROADPEAK, BW, TSV
Series
Accession:
GSE118633
ID:
200118633
11.

Recapitulation of human premature aging by using iPSCs from Hutchinson-Gilford progeria syndrome

(Submitter supplied) Hutchinson-Gilford progeria syndrome (HGPS) is a rare and fatal human premature aging disease1-5, characterized by premature atherosclerosis and degeneration of vascular smooth muscle cells (SMCs)6-8. HGPS is caused by a single-point mutation in the LMNA gene, resulting in the generation of progerin, a truncated mutant of lamin A. Accumulation of progerin leads to various aging-associated nuclear defects including disorganization of nuclear lamina and loss of heterochromatin9-12. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS3892
Platform:
GPL570
10 Samples
Download data: CEL
Series
Accession:
GSE24487
ID:
200024487
12.
Full record GDS3892

Induced pluripotent stem cell-based accelerated aging model

Analysis of iPSCs generated from fibroblasts from patients with Hutchinson-Gilford progeria syndrome (HGPS), a rare and fatal premature aging disease. Premature aging was recapitulated by differentiation of the HGPS-iPSCs. Results provide insight into molecular mechanisms underlying premature aging.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 3 cell line, 2 genotype/variation sets
Platform:
GPL570
Series:
GSE24487
10 Samples
Download data: CEL
13.

Gene expression profile of HGPS skin fibroblasts upon treatment with JH4

(Submitter supplied) To gain further insight into the biological effects of JH4, we investigated its impact on gene expression profiles. We defined a set of genes such as IL33, BRCA1, BLM, Rad51, IL6, IL8, and TNFSF18 whose expression is restored by JH4 treatment
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
4 Samples
Download data: CEL
Series
Accession:
GSE84147
ID:
200084147
14.

PML2-mediated thread-like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21290 GPL16791
20 Samples
Download data: BW, XLS
Series
Accession:
GSE137085
ID:
200137085
15.

PML2‐mediated thread‐like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome [ChIP-seq]

(Submitter supplied) Regular nuclear structure is critical for genome maintenance and proper gene expression, disorder of which has a causal role in aging. Accumulation of Progerin in Hutchinson-Gilford progeria syndrome (HGPS) disrupts the integrity of nuclear lamina and causes nuclear structure abnormalities, leading to premature aging. However, the nuclear structure/function relationships in HGPS cells have not been well addressed, and roles of nuclear sub-compartments for HGPS pathogenesis are rarely reported. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
2 Samples
Download data: BW
Series
Accession:
GSE137084
ID:
200137084
16.

PML2‐mediated thread‐like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome [RNA-seq]

(Submitter supplied) Regular nuclear structure is critical for genome maintenance and proper gene expression, disorder of which has a causal role in aging. Accumulation of Progerin in Hutchinson-Gilford progeria syndrome (HGPS) disrupts the integrity of nuclear lamina and causes nuclear structure abnormalities, leading to premature aging. However, the nuclear structure/function relationships in HGPS cells have not been well addressed, and roles of nuclear sub-compartments for HGPS pathogenesis are rarely reported. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21290
18 Samples
Download data: XLS
17.

Comparison of Hutchinson–Gilford Progeria Syndrome fibroblast cell lines to control fibroblast cell lines

(Submitter supplied) Hutchinson–Gilford progeria syndrome (HGPS) is a rare genetic disease with widespread phenotypic features resembling premature aging. HGPS was recently shown to be caused by dominant mutations in the LMNA gene, resulting in the in-frame deletion of 50 amino acids near the carboxyl terminus of the encoded lamin A protein. Children with this disease typically succumb to myocardial infarction or stroke caused by severe atherosclerosis at an average age of 13 years. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Datasets:
GDS1503 GDS1504
Platforms:
GPL97 GPL96
36 Samples
Download data: CEL
Series
Accession:
GSE3860
ID:
200003860
18.
Full record GDS1504

Hutchinson-Gilford progeria syndrome: fibroblast (HG-U133B)

Expression profiling of three fibroblast cell lines derived from Hutchinson-Gilford progeria syndrome (HGPS) patients. Identified changes in gene expression may provide clues to potential risk factors or factors influencing disease progression.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 6 cell line, 2 disease state sets
Platform:
GPL97
Series:
GSE3860
18 Samples
Download data: CEL
DataSet
Accession:
GDS1504
ID:
1504
19.
Full record GDS1503

Hutchinson-Gilford progeria syndrome: fibroblast (HG-U133A)

Expression profiling of three fibroblast cell lines derived from Hutchinson-Gilford progeria syndrome (HGPS) patients. Identified changes in gene expression may provide clues to potential risk factors or factors influencing disease progression.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 6 cell line, 2 disease state sets
Platform:
GPL96
Series:
GSE3860
18 Samples
Download data: CEL
DataSet
Accession:
GDS1503
ID:
1503
20.

Lamin B1 depletion in senescent cells leads to large-scale changes in the chromatin landscape

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL10999 GPL11154 GPL570
27 Samples
Download data: BW, CEL
Series
Accession:
GSE36641
ID:
200036641
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