Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Temporal regulation of gene expression through integration of dynamics and modifications

ABSTRACT: Temporal regulation of gene expression through integration of dynamics and modifications

PROVIDER: PRJNA1078898 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28038139_1.fastq.gz	Fastqsanger.gz
	SRR28038139_2.fastq.gz	Fastqsanger.gz
	SRR28038140_1.fastq.gz	Fastqsanger.gz
	SRR28038140_2.fastq.gz	Fastqsanger.gz
	SRR28038141_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 80

Similar Datasets

Temporal regulation of gene expression through integration of dynamics and modifications

Project description:The master regulator of the DNA damage response, the transcription factor p53, orchestrates multiple downstream responses and coordinates repair processes. In response to double-strand DNA breaks, p53 exhibits pulses of expression, but how it achieves temporal coordination of downstream responses remains unclear. Here, we show that p53's post-translational modification state is altered between its first and second pulses of expression. We show that acetylations at two sites, K373 and K382, reduced in the second pulse and these acetylations differentially affected p53 target genes, resulting in changes in gene expression programs over time. This interplay between dynamics and modification may offer a strategy for cellular hubs like p53 to temporally organize multiple processes in individual cells.

2024-10-05 | GSE256300 | GEO

Temporal regulation of gene expression through integration of p53 dynamics and modifications.

Project description:The master regulator of the DNA damage response, the transcription factor p53, orchestrates multiple downstream responses and coordinates repair processes. In response to double-strand DNA breaks, p53 exhibits pulses of expression, but how it achieves temporal coordination of downstream responses remains unclear. Here, we show that p53's posttranslational modification state is altered between its first and second pulses of expression. We show that acetylations at two sites, K373 and K382, were reduced in the second pulse, and these acetylations differentially affected p53 target genes, resulting in changes in gene expression programs over time. This interplay between dynamics and modification may offer a strategy for cellular hubs like p53 to temporally organize multiple processes in individual cells.

| S-EPMC11506164 | biostudies-literature

Reconstructing Epigenomic Dynamics through a Single-Cell Multi-Epigenome Data Integration Framework

Project description:Transcriptional regulation arises from the dynamic and combinatorial actions of multiple regulatory factors on genomic DNA. Although many epigenomic regulators have been identified, the precise order in which these factors accumulate at individual gene loci to activate transcription remains unclear. Here we show a single-cell data integration framework that infers the binding order of multiple chromatin factors at single-cell resolution. Central to this framework is sci-mtChIL-seq, a scalable single-cell method that simultaneously profiles genome-wide binding of RNA polymerase II (RNAPII) and diverse epigenomic regulators. By defining transcriptional states through RNAPII occupancy and integrating multiple sci-mtChIL-seq datasets, we systematically link the combinatorial patterns of transcription factor binding, histone modifications and chromatin remodeling. This framework reveals the temporal coordination among chromatin factors during transcriptional activation, providing a powerful approach to uncover context-dependent epigenomic dynamics and the principles of gene regulation in complex cellular systems.

2025-11-11 | GSE266320 | GEO

Temporal dynamics grapevine rootstocks

Project description:Temporal dynamics - grapevine rootstocks Raw sequence reads

| PRJNA776141 | ENA

Resolving single-cell gene expression by pseudo-temporal integration of transcriptomic and proteomic datasets.

Project description:One of the greatest prospects of multimodal single-cell analysis is the ability to integrate single-cell transcriptomic and proteomic datasets to compare transcription and translation profiles to investigate regulation between phenotypes. However, the integration of these complex datasets remains challenging. In this study, we demonstrate the use of pseudo-temporal cell orders as a mutual axis for integrating of scRNA-Seq and scp-MS data. We collected temporal samples of HEK293F cells undergoing hypoxia to isolate the variance of hypoxia from the tightly coupled variance of cell cycle. Markers for hypoxia were then used to construct pseudo-temporal orders in each dataset which were used to reveal transcription and translation dynamics of attenuated respiration in single cells. This approach allowed us to integrate single-cell transcriptomics and proteomics methods to understand the regulatory mechanisms governing biological phenotypes.

2024-12-01 | GSE273172 | GEO

Temporal dynamics of intragenomic coevolution

Project description:Temporal dynamics of bacteria-plasmid coevolution under antibiotic selection

| PRJEB28173 | ENA

Reconstructing Epigenomic Dynamics through a Single-Cell Multi-Epigenome Data Integration Framework

Project description:Reconstructing Epigenomic Dynamics through a Single-Cell Multi-Epigenome Data Integration Framework

| PRJNA1106746 | ENA

Temporal dynamics of macrophage heterogeneity after myocardial infarction

Project description:In this study, we attempted to identify the heterogeneity and temporal dynamics of leukocytes at single-cell level in mouse heart after inducing MI using the longitudinal single-cell RNA sequencing and spatial transcriptome sequencing.

2022-06-19 | GSE163129 | GEO

Temporal dynamics of gut microbiomes in urban Amazonia

Project description:Temporal dynamics of gut microbiomes in urban Amazonia

| PRJEB58722 | ENA

Temporal dynamics of macrophage heterogeneity after myocardial infarction

Project description:Temporal dynamics of macrophage heterogeneity after myocardial infarction

| PRJNA685038 | ENA