Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space

ABSTRACT: Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space

PROVIDER: PRJNA1025234 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26284381.fastq.gz	Fastqsanger.gz
	SRR26284382.fastq.gz	Fastqsanger.gz
	SRR26284383.fastq.gz	Fastqsanger.gz
	SRR26284384.fastq.gz	Fastqsanger.gz
	SRR26284385.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 65

Similar Datasets

Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [RNA-seq]

Project description:Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [RNA-seq]

| PRJNA1024100 | ENA

Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [4C-seq]

Project description:Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [4C-seq]

| PRJNA1025235 | ENA

Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [RNA-seq]

Project description:Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumor. Ionizing radiation (IR) induces dose- specific variations in transcriptional programs, implicating they are tightly regulated and critical components in the tumor response and survival. Yet, our understanding of the downstream molecular events triggered by lethal vs sublethal IR doses is limited. Herein, we report that variations in the genetic programs are positively and functionally correlated with the exposure to lethal or sublethal IR doses. Genome architecture analysis revealed that gene regulation is spatially and temporally coordinated with DNA repair kinetics. Radiation-activated genes were pre-positioned in active sub-nuclear compartments and were up-regulated following DNA damage response, while the DNA repair activity shifted to the inactive heterochromatic spatial compartments. The IR dose affected the levels of DNA damage repair and transcription modulation, but not the order of events, which was linked to their spatial nuclear positioning. Thus, distinct coordinated temporal dynamics of DNA damage repair and transcription reprogramming in the active and inactive sub-nuclear compartments highlight the importance of high-order genome organization in synchronizing the molecular events following IR.

2024-01-29 | GSE244666 | GEO

Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [4C-seq]

2024-01-29 | GSE244868 | GEO

Dose-Dependent Transcriptional Response to Ionizing Radiation Is Orchestrated with DNA Repair within the Nuclear Space.

Project description:Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumors. Ionizing radiation (IR) induces dose-specific variations in transcriptional programs, implicating that they are tightly regulated and critical components in the tumor response and survival. Yet, our understanding of the downstream molecular events triggered by effective vs. non-effective IR doses is limited. Herein, we report that variations in the genetic programs are positively and functionally correlated with the exposure to effective or non-effective IR doses. Genome architecture analysis revealed that gene regulation is spatially and temporally coordinated with DNA repair kinetics. The radiation-activated genes were pre-positioned in active sub-nuclear compartments and were upregulated following the DNA damage response, while the DNA repair activity shifted to the inactive heterochromatic spatial compartments. The IR dose affected the levels of DNA damage repair and transcription modulation, but not the order of the events, which was linked to their spatial nuclear positioning. Thus, the distinct coordinated temporal dynamics of DNA damage repair and transcription reprogramming in the active and inactive sub-nuclear compartments highlight the importance of high-order genome organization in synchronizing the molecular events following IR.

| S-EPMC10815587 | biostudies-literature

Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-01-29 | GSE244869 | GEO

Transcription profiling by array of human lymphocytes treated with a low dose of ionizing radiation

Project description:Effect of low dose ionizing radiation on gene expression profile in human lymphocytes.

2013-05-11 | E-MEXP-2918 | biostudies-arrayexpress

Identification of DNA methylation biomarkers for evaluating cardiovascular disease risk from epigenome profiles altered by low-dose ionizing radiation

Project description:DNA methylation biomarkers for evaluating cardiovascular disease risk from epigenome profiles altered by low-dose ionizing radiation

2025-10-23 | GSE246076 | GEO

Effects of Continuous in situ Low-Dose Ionizing Radiation Exposure on Pseudomonas putida KT2440

Project description:The ability to detect trace amounts of ionizing radiation is a paramount concern for chemical, biological, radiological, nuclear, and explosives (CBRNE) operations and observation of clandestine activities in the event of source relocation and contamination. Microbes respond to environmental stress such as fluctuations in pH and temperature, nutrient limited conditions, and oxidative stress with morphological and behavioral changes, and induced responses are known to persist after the stressor is removed. Innate responses to other external stressors like exposure to low-dose ionizing radiation could be measured and characterized by changes in gene expression and resulting transcriptional changes could by engineered into biosensors to monitor and discern the presence and type of radiation, respectively, in the environment. The current understanding of the biological and transcriptional responses of bacteria to various doses of ionizing radiation is minimal. The work in this study expands upon the findings in our previous study of the response of a model bacterium to low doses of ionizing radiation soil bacterium, Pseudomonas putida KT2440. Following exposure to an approximate absorbed dose rate of 9 mGy d-1 of a 239Pu, 3H, or 55Fe source, RNA-seq analysis revealed key changes in gene expression of P. putida of genes encoding membrane components, central carbon metabolism, DNA repair pathways, and motility. Several genes were differentially expressed genes in P. putida after exposure to multiple radionuclide sources. Moreover, other genes were uniquely differentially expressed by a single radionuclide source. These findings expand upon the limited understanding of the biological response to low doses of ionizing radiation and provide fundamental characterization required to develop discriminatory RNA-based biosensors.

2025-03-31 | GSE213139 | GEO

Tumorgenic properties of high-dose ionizing radiation of primary cancer-associated fibroblasts

Project description:In the context of radiotherapy, the effects elicited by ionizing radiation on the supportive stroma of tumors remains understudied. Tumor infiltrating fibroblasts are abundantly found in the stromal tissue of most tumor types and are key determinants of tumor progression and metastasis. Given the clinical attention that ablative radiotherapy is gaining nowadays, and the paramount role played by CAFs in cancer sustainability, in this study the effect of high-dose ionizing radiation on primary CAF?S have been investigated. We have used high-throughput transcriptome analysis to ascertain in which degree tumor stromal fibroblast become pro-tumorigenic or anti-tumorigenic after ablative irradiation. Hence, genome-wide transcriptome analysis has been carried out on CAFs isolated from NSCLC tumors after receiving a single dose of 18 Gray. The expressions of relevant genes have been validated by real-time PCR, and transformed cellular pathways have been checked by functional assays. Overall, our data reveals profound changes in biological pathways including cellular stress, DNA damage, cell cycle, aging, apoptosis, oxidative stress, and matrix remodeling. Ablative radiation doses may exert both pro-and anti-tumorigenic effects on CAFs. The ultimate effect of such disturbances merits further investigation in more complex in vivo settings.

2012-04-16 | GSE37318 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data