Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated multi-omics approach revealed cellular senescence landscape

ABSTRACT: Integrated multi-omics approach revealed cellular senescence landscape

PROVIDER: PRJNA865031 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20746221_1.fastq.gz	Fastqsanger.gz
	SRR20746221_2.fastq.gz	Fastqsanger.gz
	SRR20746222_1.fastq.gz	Fastqsanger.gz
	SRR20746222_2.fastq.gz	Fastqsanger.gz
	SRR20746223_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Integrated multi-omics approach revealed cellular senescence landscape

2022-08-15 | GSE210285 | GEO

Integrated multi-omics approach revealed cellular senescence landscape.

Project description:Cellular senescence is a complex multifactorial biological phenomenon that plays essential roles in aging, and aging-related diseases. During this process, the senescent cells undergo gene expression altering and chromatin structure remodeling. However, studies on the epigenetic landscape of senescence using integrated multi-omics approaches are limited. In this research, we performed ATAC-seq, RNA-seq and ChIP-seq on different senescent types to reveal the landscape of senescence and identify the prime regulatory elements. We also obtained 34 key genes and deduced that NAT1, PBX1 and RRM2, which interacted with each other, could be the potential markers of aging and aging-related diseases. In summary, our work provides the landscape to study accessibility dynamics and transcriptional regulations in cellular senescence. The application of this technique in different types of senescence allows us to identify the regulatory elements responsible for the substantial regulation of transcription, providing the insights into molecular mechanisms of senescence.

| S-EPMC9638896 | biostudies-literature

Integrated multi-omics analysis

Project description:Integrated multi-omics analysis

| PRJNA1069651 | ENA

Prediction of gene activity based on an integrated multi-omics approach.

Project description:An increasingly common method for predicting gene activity is genome-wide chromatin immunoprecipitation of M-bM-^@M-^XactiveM-bM-^@M-^Y chromatin modifications followed by massively parallel sequencing (ChIP-seq). Using a novel ChIP-seq quantification method (cRPKM), we tested the power of such ChIP-seq strategies to predict relative protein and RNA levels at the pre-pro-B and pro-B differentiation stages in early B cell lymphopoiesis. Using a multi-omics approach that compares promoter chromatin status (ChIP-seq; published in GSE:21978) with ongoing active transcription (GRO-seq; published in GSE:40173), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ), we demonstrate that active chromatin modifications at promoters are a good indicator of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted differentially expressed proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in expression of their cognate proteins. This large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Interestingly, the most differentially expressed protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by an identified miRNA. These data provide a striking example of how our integrated multi-omics data set can be useful in uncovering regulatory mechanisms. Total RNA from mouse pre-pro-B and pro-B cells, depleted of rRNA and small RNAs, was sequenced using a strand specific, single end sequencing strategy.

2013-11-19 | E-GEOD-52450 | biostudies-arrayexpress

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Project description:An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

| PRJNA644384 | ENA

Prediction of gene activity based on an integrated multi-omics approach.

Project description:An increasingly common method for predicting gene activity is genome-wide chromatin immunoprecipitation of ‘active’ chromatin modifications followed by massively parallel sequencing (ChIP-seq). Using a novel ChIP-seq quantification method (cRPKM), we tested the power of such ChIP-seq strategies to predict relative protein and RNA levels at the pre-pro-B and pro-B differentiation stages in early B cell lymphopoiesis. Using a multi-omics approach that compares promoter chromatin status (ChIP-seq; published in GSE:21978) with ongoing active transcription (GRO-seq; published in GSE:40173), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ), we demonstrate that active chromatin modifications at promoters are a good indicator of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted differentially expressed proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in expression of their cognate proteins. This large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Interestingly, the most differentially expressed protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by an identified miRNA. These data provide a striking example of how our integrated multi-omics data set can be useful in uncovering regulatory mechanisms.

2013-11-19 | GSE52450 | GEO

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

Project description:An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

| PRJNA670168 | ENA

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq) [RNA-seq]

Project description:An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq) [RNA-seq]

| PRJNA670209 | ENA

Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells

Project description:Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells

| PRJNA495397 | ENA

Harnessing HetHydrogel: An Approach to Single-Cell Multi-Omics

Project description:Harnessing HetHydrogel: An Approach to Single-Cell Multi-Omics