Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cellular fractionation reveals transcriptome responses of human fibroblasts to UV-C irradiation

ABSTRACT: Cellular fractionation reveals transcriptome responses of human fibroblasts to UV-C irradiation

PROVIDER: PRJNA735643 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14746331_1.fastq.gz	Fastqsanger.gz
	SRR14746331_2.fastq.gz	Fastqsanger.gz
	SRR14746332_1.fastq.gz	Fastqsanger.gz
	SRR14746332_2.fastq.gz	Fastqsanger.gz
	SRR14746333_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Cellular fractionation reveals transcriptome responses of human fibroblasts (MRC5_VA cells and CS1AN cells) to UV-C irradiation

Project description:Cellular fractionation reveals transcriptome responses of human fibroblasts (MRC5_VA cells and CS1AN cells) to UV-C irradiation

| PRJNA764527 | ENA

Cellular fractionation reveals transcriptome responses of human fibroblasts to UV-C irradiation

Project description:The response to DNA damage intersects with many other physiological processes in the cells, including initiation of DNA repair, regulation of transcription and translation, chromatin remodeling, and the cell cycle regulation to contend with the challenge. Transcription shutdown is not simply a consequence of the physical arrest of RNA polymerase II by DNA lesions, but also could be elicited by signaling in trans. While to date many of the specific molecular events are not fully elucidated. What is the signal that operates in trans to slow transcriptional elongation globally? Which factors are required for transcription restart after DNA repair? How is TC-NER controlled by the multifaceted transcriptional response? In this study, we sought to map the transcription restart and isolate the set of lncRNAs that are likely to function at the chromatin interface by using biochemical fractionation of the cellular compartment coupled to RNA-seq.

2021-06-08 | GSE176258 | GEO

Cellular fractionation reveals transcriptome responses of human fibroblasts (MRC5_VA cells and CS1AN cells) to UV-C irradiation

Project description:Cells activate a multifaceted DNA damage response to remove transcription-blocking DNA lesions, The genome-wide reduction of RNA synthesis and the paradoxical continuous loading of RNAP II at initiation sites is still poorly understood. Uncovering how dramatic changes to the transcriptional program contribute to TC-NER (transcription-coupled nucleotide excision repair) comprises one of the most fascinating frontiers in DNA repair research. Here we examined UV-induced gene regulation in human fibroblasts by performing RNA-seq with fractionated chromatin-associated and cytoplasmic transcripts. This approach allowed us to separate the synthesis of nascent transcripts from the accumulation of mature RNAs. In addition to documenting the subcellular locations of coding transcripts, our results also provide a high-resolution view of the transcription activities of noncoding RNAs in response to cellular stress. At the same time, the data showed that vast majority of chromatin-enriched DNA damage response transcripts are cis-acting. Distinct from coding genes that transcripts with shorter length are prefered to be recovered first, repression of lncRNA transcription after UV exposure is inactivated first on noncoding transcripts with longer length. This work provides an updated framework for cellular RNA organization in response to stress and may prove useful in understanding how cells respond to transcription-blocking DNA damage.

2021-09-22 | GSE184408 | GEO

UV irradiation treatment

Project description:UV irradiation treatment Metagenome

| PRJNA688797 | ENA

Cellular fractionation reveals transcriptome responses of human fibroblasts to UV-C irradiation.

Project description:While cells activate a multifaceted DNA damage response to remove transcription-blocking DNA lesions, mechanisms to regulate genome-wide reduction of RNA synthesis and the paradoxical continuous loading of RNAP II at initiation sites are still poorly understood. Uncovering how dramatic changes to the transcriptional program contribute to TC-NER (transcription-coupled nucleotide excision repair) is important in DNA repair research. However, the functional significance of transcriptome dynamics and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we examined UV-induced gene expression regulation in human fibroblasts by performing RNA-seq with fractionated chromatin-associated and cytoplasmic transcripts. This approach allowed us to separate the synthesis of nascent transcripts from the accumulation of mature RNAs. In addition to documenting the subcellular locations of coding transcripts, our results also provide a high-resolution view of the transcription activities of noncoding RNAs in response to cellular stress. At the same time, the data showed that vast majority of genes exhibit large changes in chromatin-associated nascent transcripts without corresponding changes in cytoplasmic mRNA levels. Distinct from protein-coding genes that transcripts with shorter length prefer to be recovered first, repression of lncRNA transcription after UV exposure is inactivated first on noncoding transcripts with longer length. This work provides an updated framework for cellular RNA organization in response to stress and may provide useful information in understanding how cells respond to transcription-blocking DNA damage.

| S-EPMC8873393 | biostudies-literature

Efficient cellular fractionation of RNA

Project description:Efficient cellular fractionation of RNA

| PRJEB4845 | ENA

MRG15 interactome upon UV irradiation

Project description:The aim of this analysis is to identify the difference between interaction partners of MRG15 wild type and Chromodomain and MRG domain mutants upon UV irradiation. Therefore, MRG15 wild type and mutants (N-terminal FLAG tag) were overexpressed in U2OS cells. After UV irradiation, immunoprecipitation of the constructs was performed using FLAG M2 affinity gel. The constructs were eluted from the beads with 3xFLAG peptide.

2023-07-03 | PXD043089 | Pride

Transcriptional responses to UV irradiation in CS-B cells

Project description:Cockayne syndrome B (CSB) protein is a member of the SWI/SNF family and has DNA-dependent ATPase and ATP-dependent chromatin remodeling activities. The CSB protein is missing or altered in CS-B cells. CS-B cells are hypersensitive to UV light and defective in transcription-coupled DNA repair (TCR). TCR efficiently removes a variety of lesions from the transcribed strand of active genes. It has been shown that lesions specifically in the transcribed strand of active genes trigger the induction of apoptosis following UV irradiation. Several DNA damage signaling cascades, including the ATR/Chk1, p38 kinase, p53, and jun N-terminal kinase pathways are activated following UV irradiation. However, the role of TCR in cellular global transcriptional responses to UV irradiation remains to be elucidated. Using oligonucleotide microarray technology, we analyzed the time course of responses of CS-B cells (CS-B) and CS-B cells complemented with wild-type CSB cDNA (CS-B wt). Keywords: UV response, time course, disease state analysis

2007-09-10 | GSE8939 | GEO

Pea seedlings under UV-B irradiation

Project description:To investigate the mechanistic effects of UV irradiation on pea seedlings at the protein level, proteomic analyses were performed on pea seedlings irradiated daily with 0 and 10 min UV-B.

2023-05-04 | PXD038486 | Pride

water sample after uv irradiation

Project description:water sample after uv irradiation Raw sequence reads

| PRJNA679675 | ENA