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Items: 1 to 20 of 71829

1.

High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression [Long Read DNA-seq]

(Submitter supplied) This study presents the highest-resolution chromatin map of cellular senescence to date, shedding light on how genomic architecture is altered with this damaging phenotype. Senescence, a driver of aging, is a pro-inflammatory state of proliferative arrest caused by DNA damage; it is associated with epigenetic changes, including those to chromatin organization. We created ~3kb Hi-C contact maps of proliferating, quiescent, and replicative senescent lung fibroblasts, and also compared these to oncogene-induced senescence. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL26167
2 Samples
Download data: BED
Series
Accession:
GSE268488
ID:
200268488
2.

Methylomic signatures of tau and beta amyloid in transgenic mouse models of Alzheimer’s disease neuropathology

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Mus musculus; Rattus norvegicus
Type:
Methylation profiling by array; Methylation profiling by high throughput sequencing
Platforms:
GPL28271 GPL17021
283 Samples
Download data: IDAT
Series
Accession:
GSE246561
ID:
200246561
3.

Methylomic signatures of tau and beta amyloid in transgenic mouse models of Alzheimer’s disease neuropathology [RRBS]

(Submitter supplied) We identified widespread DNA methylation changes associated with the development of both tau and amyloid neuropathology, including differentially methylated positions (DMPs) and regions (DMRs) at loci previously implicated in AD and overlapping changes identified in our ongoing analyses of human post-mortem AD brains.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL17021
124 Samples
Download data: CSV
Series
Accession:
GSE246560
ID:
200246560
4.

Methylomic signatures of tau and beta amyloid in transgenic mouse models of Alzheimer’s disease neuropathology [HorvathMammalMethylChip40 Methylation Beadchip]

(Submitter supplied) We identified widespread DNA methylation changes associated with the development of both tau and amyloid neuropathology, including differentially methylated positions (DMPs) and regions (DMRs) at loci previously implicated in AD and overlapping changes identified in our ongoing analyses of human post-mortem AD brains.
Organism:
Homo sapiens; Mus musculus; Rattus norvegicus
Type:
Methylation profiling by array
Platform:
GPL28271
159 Samples
Download data: CSV, IDAT
Series
Accession:
GSE246559
ID:
200246559
5.

H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells (CUT&RUN)

(Submitter supplied) The histone variant H3.3 facilitates mRNA transcription activation and suppression at cis-regulatory elements such as promoters and enhancers, with histone epigenetic modifications including acetylation or methylation as context-defining features. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting transcription features and with more recent evidence suggesting that these modifications may influence transcription. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
28 Samples
Download data: BED, BW
Series
Accession:
GSE272577
ID:
200272577
6.

H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells (TT-Seq)

(Submitter supplied) The histone variant H3.3 facilitates mRNA transcription activation and suppression at cis-regulatory elements such as promoters and enhancers, with histone epigenetic modifications including acetylation or methylation as context-defining features. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting transcription features and with more recent evidence suggesting that these modifications may influence transcription. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30172
8 Samples
Download data: BW, TXT
Series
Accession:
GSE272575
ID:
200272575
7.

Epigenetic Dysregulation of H19/IGF2 in Hepatic Cells Exposed to Toxic Metal Mixtures In Vitro [RNA-seq]

(Submitter supplied) Exposure to mixtures of toxic metals is known to cause adverse health effects through epigenetic alterations. Here we aimed to examine the unexplored area of aberrant DNA methylation in the H19/IGF2 domain following combined toxic metal exposure. An in vitro epigenotoxicity assay using the human normal liver epithelial cell line THLE-3 was conducted. When THLE-3 cells were exposed to specific concentrations of either organic arsenic or MeHgCl, an increase in the H19 lncRNA levels and a marked reduction in the IGF2 mRNA levels were observed. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: TXT
Series
Accession:
GSE280026
ID:
200280026
8.

Epigenetic Dysregulation of H19/IGF2 in Hepatic Cells Exposed to Toxic Metal Mixtures In Vitro [Bisulfite-seq]

(Submitter supplied) Exposure to mixtures of toxic metals is known to cause adverse health effects through epigenetic alterations. Here we aimed to examine the unexplored area of aberrant DNA methylation in the H19/IGF2 domain following combined toxic metal exposure. An in vitro epigenotoxicity assay using the human normal liver epithelial cell line THLE-3 was conducted. When THLE-3 cells were exposed to specific concentrations of either organic arsenic or MeHgCl, an increase in the H19 lncRNA levels and a marked reduction in the IGF2 mRNA levels were observed. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL15520
42 Samples
Download data: TXT
Series
Accession:
GSE280025
ID:
200280025
9.

2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [RNA-seq]

(Submitter supplied) We developed a new technique by supplementing carrier materials during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using 2cChIP-seq, we generated high-quality epigenomic profiles of histone modifications and DNA methylation in 10-1,000 cells. Moreover, 2cChIP-seq reliably captures genomic regions with histone modification at single-cell level. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21273
2 Samples
Download data: TXT
Series
Accession:
GSE186681
ID:
200186681
10.

2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [2cMeDIP-seq]

(Submitter supplied) We developed a new technique by supplementing carrier materials during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using 2cChIP-seq, we generated high-quality epigenomic profiles of histone modifications and DNA methylation in 10-1,000 cells. Moreover, 2cChIP-seq reliably captures genomic regions with histone modification at single-cell level. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL21273
3 Samples
Download data: BW
Series
Accession:
GSE186680
ID:
200186680
11.

2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [2cChIP-seq and 2cMeDIP-seq]

(Submitter supplied) We developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10–1,000 cells. more...
Organism:
Homo sapiens; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL21273 GPL20795
34 Samples
Download data: BW
Series
Accession:
GSE173281
ID:
200173281
12.

2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [single-cell 2cChIP-seq]

(Submitter supplied) We developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10–1,000 cells. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
192 Samples
Download data: BW
Series
Accession:
GSE165509
ID:
200165509
13.

Investigating DNA methylation in individuals with pathogenic variants in SCN1A

(Submitter supplied) SCN1A, encoding the sodium channel protein type 1 alpha subunit, is the most implicated gene in epilepsy. Pathogenic loss-of-function variants that result in SCN1A haploinsufficiency cause the most common DEE, known as Dravet syndrome (DS). Pathogenic gain-of-function variants have been found to cause a more severe, early-onset epilepsy syndrome that is distinct from DS. Here, we investigated DNA methylation patterns in these individuals with SCN1A variants.
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL21145
45 Samples
Download data: IDAT, RDS
Series
Accession:
GSE280241
ID:
200280241
14.

H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium [cutandtag_enzyme_profiling]

(Submitter supplied) Cell plasticity is needed during development and homeostasis to generate diverse cell types from stem and progenitor cells. Following differentiation, plasticity must be restricted in specialized cells to maintain tissue integrity and function. For this reason, specialized cell identity is highly stable under homeostatic conditions; however, cells in some tissues regain plasticity during injury-induced regeneration. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
12 Samples
Download data: BW
Series
Accession:
GSE275296
ID:
200275296
15.

H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium [regen_cutandtag_mouse]

(Submitter supplied) Cell plasticity is needed during development and homeostasis to generate diverse cell types from stem and progenitor cells. Following differentiation, plasticity must be restricted in specialized cells to maintain tissue integrity and function. For this reason, specialized cell identity is highly stable under homeostatic conditions; however, cells in some tissues regain plasticity during injury-induced regeneration. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
18 Samples
Download data: BW
Series
Accession:
GSE275295
ID:
200275295
16.

H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium [regen_rnaseq_mouse]

(Submitter supplied) Cell plasticity is needed during development and homeostasis to generate diverse cell types from stem and progenitor cells. Following differentiation, plasticity must be restricted in specialized cells to maintain tissue integrity and function. For this reason, specialized cell identity is highly stable under homeostatic conditions; however, cells in some tissues regain plasticity during injury-induced regeneration. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
6 Samples
Download data: TSV
Series
Accession:
GSE275294
ID:
200275294
17.

Bulk RNA-sequencing of wild-type (Ler) and dme-2 calli harvested 7 days after incubation on callus-inducing medium and of de novo regenerated shoots harvested 14 days after incubation on shoot-inducing medium

(Submitter supplied) Plants possess high potential for somatic cell reprogramming. Despite extensive studies on the molecular network and key genetic factors during regeneration, the underlying epigenetic landscape remains incompletely understood. Here, we explored methylome and transcriptome dynamics during two-step plant regeneration. During leaf-to-callus transition, genic CG methylation shifts, while pericentromeric regions undergo substantial CG and extensive CHH hypomethylation. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26208
12 Samples
Download data: TSV
Series
Accession:
GSE269609
ID:
200269609
18.

Transcriptome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [RNA-seq]

(Submitter supplied) UHRF1 maintains DNA methylation by recruiting DNA methyltransferases (DNMT’s) to chromatin. These dynamics are well defined for mouse STELLA (mSTELLA) but poorly characterized for human STELLA (hSTELLA). Herein, we demonstrate that hSTELLA is defective, while mSTELLA is fully proficient in associating with UHRF1 and inhibiting the abnormal DNA methylation and oncogenic functions of UHRF1 in human cancer cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
51 Samples
Download data: TXT
Series
Accession:
GSE255105
ID:
200255105
19.

DNA Methylome Analysis of Human Cancer Cells with Depleted or Overexpressed STELLA Proteins [Array]

(Submitter supplied) Genome-wide DNA methylation profiling of the human STELLA (hSTELLA) knockout cell clones derived from TGCT cell lines (BeWo and NCCIT). The DNA methylome profiles are also studied on the CRC cells lines (HCT116 and RKO) stably expressing hSTELLA and mouse STELLA (mSTELLA), as well as on the HCT116 cells treated by LNP-delivered mRNA encoding mSTELLA. The Infinium MethylationEPIC 850k array was used to obtain DNA methylation profiles across more than 850,000 CpGs in 26 samples. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL21145
26 Samples
Download data: IDAT, TXT
Series
Accession:
GSE255083
ID:
200255083
20.

H3K36 methylation regulates cell plasticity and regeneration in the intestinal epitheliumm (RNA-seq IV)

(Submitter supplied) Cell plasticity is needed during development and homeostasis to generate diverse cell types from stem and progenitor cells. Following differentiation, plasticity must be restricted in specialized cells to maintain tissue integrity and function. For this reason, specialized cell identity is highly stable under homeostatic conditions; however, cells in some tissues regain plasticity during injury-induced regeneration. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
12 Samples
Download data: TSV
Series
Accession:
GSE249088
ID:
200249088
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