Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria using 5PSeq

ABSTRACT: Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria using 5PSeq

PROVIDER: PRJNA957826 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24233900.fastq.gz	Fastqsanger.gz
	SRR24233901.fastq.gz	Fastqsanger.gz
	SRR24233852.fastq.gz	Fastqsanger.gz
	SRR24233853.fastq.gz	Fastqsanger.gz
	SRR24233854.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 53

Similar Datasets

Analysing environmentally induced genome-wide frameshift

Project description:Analysing environmentally induced genome-wide frameshift

| PRJNA957825 | ENA

Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria using 5PSeq

Project description:In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation.To explore this process, we utilized HT-5PSeq (Zhang & Pelechano, 2021, PMID:35474692) to measure the ribosome footprint of co-translationally degraded mRNAs in S.cerevisiae under different stresses in YPD and CSM (poor nutrients). To show the mechanism is conserved in bacteria, we performed HT-5PSeq in B.subtilis upon starvation .Our goal with HT-5PSeq is to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

2025-05-14 | GSE230202 | GEO

Analysing environmentally induced genome-wide frameshift in S. cerevisiae using ribosome profiling

Project description:Analysing environmentally induced genome-wide frameshift in S. cerevisiae using ribosome profiling

| PRJNA957827 | ENA

Analysing environmentally induced genome-wide frameshift in S. cerevisiae using SLAM-Seq

Project description:Analysing environmentally induced genome-wide frameshift in S. cerevisiae using SLAM-Seq

| PRJNA957829 | ENA

Analysing environmentally induced genome-wide frameshift in S. cerevisiae using SLAM-Seq

Project description:In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To measure the RNA degradation, we utilized SLAM-seq (Herzog, et.al, 2017, PMID: 28945705) in S.cerevisiae in wildtype and NMD mutant (upf1Δ). Our goal with SLAM-seq is to quantify the fraction of the transcriptome that is directly degraded as a result of environmentally induced ribosome frameshifts through an NMD-dependent mechanism.

2025-05-14 | GSE230204 | GEO

Analysing environmentally induced genome-wide frameshift

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

2025-05-14 | GSE230205 | GEO

Analysing environmentally induced genome-wide frameshift in S. cerevisiae using ribosome profiling

Project description:In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To explore this process, we utilized Ribosome profiling (Ingolia, et.al 2009, PMID: 19213877), in S.cerevisiae in low nutrients condition. Our goal with Ribosome profiling was to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

2025-05-14 | GSE230203 | GEO

Detection of cryptic start codons in set2D by 5PSeq

Project description:We investigated cryptic transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We used 5PSeq approach, which measures ribosome dynamics by sequencing the presence of co-translation mRNA degradation intermediates, to assess if cryptic transcripts are engaged in active translation. We show that chromatin-dependent cryptic transcripts can be recognized by ribosomes and have the potential to produce truncated polypeptides by using downs-stream, in-frame start codons. Our work suggests that a significant fraction of chromatin-dependent internal cryptic promoters are in fact alternative truncated mRNA isoforms.

2019-10-01 | GSE118758 | GEO

Development of High-throughput 5Pseq and detection of ribosome stalls at termination level in Saccharomyces cerevisiae

Project description:We developed a high throughput 5’P sequencing approach (HT-5PSeq) to investigate 5'P mRNA degradome in relation with translation process. This approach is easy and scalable; and uses an affordable rRNA depletion based on duplex-specific nuclease treatment. We use it to investigate in vivo ribosome stalls in S. cerevisiae and S. pombe at single nucleotide resolution. We investigate the 5’P degradation profiles associated to ribosome pausing, its regulation in stress conditions and the relative poly(A) length of mRNA degradation intermediates.

2021-04-02 | GSE152375 | GEO

programmed ribosomal frameshift

Project description:programmed ribosomal frameshift Raw sequence reads

| PRJNA310019 | ENA