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Nanopore long-read RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

ABSTRACT: Nanopore long-read RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

PROVIDER: PRJNA1163900 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30762256_1.fastq.gz	Fastqsanger.gz
	SRR30762257_1.fastq.gz	Fastqsanger.gz
	SRR30762258_1.fastq.gz	Fastqsanger.gz
	SRR30762259_1.fastq.gz	Fastqsanger.gz
	SRR30762260_1.fastq.gz	Fastqsanger.gz

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Nanopore long-read RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

Project description:Recent completion of the telomere-to-telomere (T2T) genome assembly has enabled a comprehensive characterization of pericentromeric SatⅠ, SatII, SatⅢ and centromeric α-satellite repeats. SatⅢ DNA constitutes ~1.56% of the genome with a reported localization across 16 chromosomes. The transcription activity of SatⅢ DNA across genome and the sequence of SatⅢ transcripts remained largely unclear. We performed nanopore long-read RNA sequencing (RNA-seq) in untreated (UN), sodium arsenite (SA: 0.1mM, 5 h) and heat shock (HS: 42°C, 2 h; 37°C, 1 h) stressed HeLa cells to characterize SatⅢ transcripts . Since a portion of SatⅢ transcripts is non-polyadenylated, We performed polyadenylated (poly(A)+) and rRNA-depleted (ribo-) nanopore cDNA long-read RNA-seq.

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TSA-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

Project description:TSA-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

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ATAC-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed THP-1 cells

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RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa,HUVEC and THP-1 cells

Project description:RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa,HUVEC and THP-1 cells

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TSA-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

Project description:Mammalian cells activate diverse defense mechanisms in response to stresses. Nuclear stress bodies (nSBs) are transient membraneless organelles in primates that only form upon severe stresses. Little is known on how their formation contributes to cellular homeostasis or whether nSBs have any pathophysiological roles. We observed that the de novo formation of nSBs accompanies enlarged pericentromeric SatⅢ DNA chromatin loci, prompting us to investigate whether such an acute alteration impacts regional chromatin accessibility and gene expression. To test this, we performed an improved Tyramide Signal Amplification (TSA) mapping to identify genes proximal to newly formed nSBs.

2025-05-26 | GSE280712 | GEO

ATAC-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed THP-1 cells

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RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa,HUVEC and THP-1 cells

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Sodium arsenite effects on DNA methylation in zebrafish embryos.

Project description:There is a need to develop biomarkers in alternative testing models predictive for chemically induced chronic disease in humans, preferably describing key events and their relationships in an adverse outcome pathway analysis. Epigenetic modifications, and particularly DNA methylation effects, have been implicated as a major event in susceptibility to develop chronic disease. Arsenic exposure affects large populations around the world through drinking water and industrial activities. We sought to identify epigenetic markers of arsenic exposure. We analyzed the effect of sodium arsenite on DNA methylation in Danio rerio (zebrafish) embryos using unbiased methylation profiling by high throughput sequencing.

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Sodium arsenite induced DNA methylation changes in A549 human epithelial lung carcinoma cells

Project description:Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns Cells were exposed to sodium arsenite (NaAsO2, Sigma) at concentrations of 0.08 M-BM-5M, 0.4 M-BM-5M and 2 M-BM-5M for 1, 2 and 8 weeks. A549 arsenic dose time response study.

2014-09-17 | E-GEOD-44173 | biostudies-arrayexpress

Sodium arsenite induced gene expression changes in A549 human epithelial lung carcinoma cells

Project description:Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns which could lead to altered gene expression Cells were exposed to sodium arsenite (NaAsO2, Sigma) at concentrations of 0.08 M-BM-5M, 0.4 M-BM-5M and 2 M-BM-5M for 1, 2 and 8 weeks.

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