Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE277764 | GEO | 2025/05/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

| PRJNA1163900 | ENA

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

2025-05-26 | GSE280307 | GEO

Transcriptome analysis of TSC1 and TSC2 using Nanopore long-read sequencer

Project description:Tuberous sclerosis complex (TSC) is a relatively common autosomal dominant disorder characterized by multiple dysplastic organ lesions and neuropsychiatric symptoms, caused by loss-of-function mutation of either TSC1 or TSC2. Target-capture full-length double-stranded cDNA sequencing using long-read sequencer Nanopore (Nanopore Long-read Target Sequencing) revealed that the various kinds of the TSC1 and TSC2 full-length transcripts and the novel intron retention transcripts of TSC2 in TSC patient. Our results indicate that the Nanopore Long-read Target Sequencing is useful for the detection of mutations and confers information on the full-length alternative splicing transcripts for the genetic diagnosis.

2023-09-04 | GSE241410 | GEO

Homo sapiens

Project description:Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs

| PRJNA1186217 | ENA

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

2025-05-26 | GSE278916 | GEO

Profiling the Full-Length Transcriptome of Extracellular Vesicles With Oxford Nanopore Sequencing

Project description:While numerous studies have described the transcriptomes of EVs in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-encapsulated RNA populations. Furthermore, it has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and little is known about the extent to which full-length mRNAs are present within EVs. Using Oxford nanopore long-read RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 441 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 12.72% of all reads present in EVs corresponded to known full-length transcripts, 65.34% of which were mRNAs. We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples. Here we report a full-length transcriptome from human EVs, as determined by long-read nanopore sequencing.

2023-09-27 | GSE225471 | GEO

Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts

Project description:Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORF), six novel ORF-containing transcripts, and fifteen transcripts encoding for messages that potentially alter protein functions through truncations or fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Of these, an evolutionary conserved protein was detected containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.

2022-08-30 | PXD034464 | Pride

A nanopore long-read transcriptome in pancreatic cancer cells

Project description:This project aims to leverage Oxford Nanopore Technologies (ONT) long-read RNA sequencing to achieve a comprehensive analysis of the human pancreatic cancer transcriptome. Traditional short-read sequencing methods often struggle with accurately reconstructing full-length transcripts and discerning complex splicing events due to their limited read lengths. In contrast, ONT's long-read sequencing can generate reads that span entire RNA molecules, facilitating precise identification of transcript isoforms, alternative splicing patterns, and poly(A) tail length. By applying this technology, we seek to enhance the annotation of the pancreatic cancer transcriptome, uncover novel transcripts, and gain deeper insights into gene expression dynamics. The findings from this study have the potential to advance our understanding of gene regulation and contribute to the development of novel therapeutic strategies.

2025-07-23 | GSE293661 | GEO

Assembly of the Arabidopsis (Col-0) centromeres using Oxford Nanopore Technology long-read DNA sequencing.

Project description:Nanopore long-read sequencing was used to generate a complete assembly of the Arabidopsis centromeres.

2021-04-02 | E-MTAB-10272 | biostudies-arrayexpress