Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PAT-seq - a high-throughput polyadenylation assay for the Illumina platform

ABSTRACT: PAT-seq - a high-throughput polyadenylation assay for the Illumina platform

PROVIDER: PRJEB6043 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR472933_1.fastq.gz	Fastqsanger.gz
	ERR472933_2.fastq.gz	Fastqsanger.gz
	ERR472934_1.fastq.gz	Fastqsanger.gz
	ERR472934_2.fastq.gz	Fastqsanger.gz
	ERR472935_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

PAT-seq - a high-throughput polyadenylation assay for the Illumina platform

Project description:Polyadenylation - the cleavage of the nascent mRNA and the addition of a tract consisting of adenine bases in a non-template-dependent manner - is a post-transcriptional modification characteristic of the majority of eukaryotic transcripts. In this study we explore PAT-seq, an Illumina-based poly(A) tail assay, based on the low-throughput G-tailing approach. Briefly, our approach is based on G-tailing poly(A) selected mRNA followed by fragmentation and reverse transcription using a mixture of primers targeting the poly(A)-tail/G-tag junction and the polyadenylation site and the body of the transcripts. The resulting cDNA fragments are sequenced using standard Illumina RNA-seq protocol.

2014-04-05 | E-MTAB-2456 | biostudies-arrayexpress

E-MTAB-2456

Project description:PAT-seq - a high-throughput polyadenylation assay for the Illumina platform

2019-05-14 | E-MTAB-2456 | ExpressionAtlas

Microfluidic platform for monitoring Saccharomyces cerevisiae mutation accumulation assay

Project description:Microfluidic platform for monitoring Saccharomyces cerevisiae mutation accumulation assay

| PRJEB43850 | ENA

Setaria viridis strain:PAT-5 | cultivar:PAT-5

Project description:Setaria viridis strain:PAT-5 | cultivar:PAT-5 Genome sequencing

| PRJNA334531 | ENA

PAT-seq: a simple approach to digital gene expression, the measure of poly(A)-tail length and its position in eukaryotic transcriptomes

Project description:The Poly(A)-Tail focused RNA-seq, or PAT-seq approach, is an affordable and efficient tool for the measure of 3’UTR dynamics. We show here that PAT-seq returns (i) digital gene expression, (ii) polyadenylation site usage within and between samples, including alternative adenylation, and (iii) the polyadenylation-state the transcriptome. PAT-seq differs from previous 3’ focused RNA-seq methods in that it strictly depends on native 3’ adenylation within total RNA samples and thus removes the need for ribosome depletion and, that the full native poly(A)-tail is included in the sequencing libraries. Limited RNase digestion combined with size selection and directional sequencing mean that deep-sequencing reads map to within ~50-100 bases of adenylation sites and run from unique sequence into adenosine homopolymers. Here, total RNA samples from budding yeast cells were analyzed to highlight the changes in gene expression and adenylation-state of the transcriptome in response to loss of the deadenylase Ccr4. Furthermore, concordant changes to gene expression and adenylation-state were demonstrated in a classic Crabtree-Warburg metabolic shift. Because all adenylated RNA are interrogated by the PAT-seq approach, alternative adenylation sites, long noncoding RNA and other non-coding RNA and RNA decay intermediates were also identified.

2015-08-19 | GSE53461 | GEO

Transcriptome sequencing (RNA-Seq) of PAT cells in CAD and control patients for exploring the association between CAD and PAT

Project description:Coronary artery disease (CAD) poses a worldwide health threat. Compelling evidence shows that pericardial adipose tissue (PAT), a brown-like adipose adjacent to the external surface of the pericardium, is associated with CAD. However, the specific molecular mechanisms of PAT in CAD are elusive. For characterizing human PAT and explore its association with CAD, the transcriptome characteristics were assessed in 5 CAD patients and 4 controls via RNA-sequencing.

2021-07-30 | GSE179397 | GEO

Transcriptomical study on multipul pat mutants

Project description:The Arabidopsis genome encodes 3 PAT mRNA decapping factors: PAT1(AT1g79090), PATH1 (AT3g22270) and PATH2 (AT4g14990). We generated single, double and triple knockouts (KOs) of the three PATs by CRISPR/CAS9-mediated genome editing in the summ2-8 background to avoid immune activation. The 6 weeks-old soil-grown pat triple mutants exhibited markedly stunted growth compared to the other pat single or double mutants indicating functional redundancy of PATs in regulating plant development. To identify genes which affect different developmental programs regulated by PATs, we performed RNA-seq from plants of pat1-1path1-4path2-1summ2-8 and all single and double mutant combinations.

2024-01-26 | GSE253757 | GEO

High-throughput transcriptomics platform for screening hepatotoxicants

Project description:We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants.

2021-09-01 | GSE152128 | GEO

RNA-seq analysis determined the effect of pat or cobB mutation on transcriptional levels in Salmonella Typhimurium 14028s.

Project description:Salmonella causes a range of diseases in different hosts, including enterocolitis and systemic infection. Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely unknown. Reversible acetylation in Salmonella Typhimurium depends on acetyltransferase Pat and nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase CobB. Here, we used cell and animal models to evaluate the virulence of pat and cobB deletion mutants in S. Typhimurium, and found that pat is essential for bacterial intestinal colonization, systemic infection and host inflammation response. Next, to understand the underlying mechanism, genome-wide transcriptome was analyzed. RNA-seq data showed the expression of Salmonella pathogenicity islands 1 (SPI-1) is partially dependent on pat. In addition, we found that HilD is a substrate of Pat, which is essential for maintaining HilD protein level. Taken together, these results suggested that protein acetylation system regulates SPI-1 expression by controlling HilD in a post-translational manner to mediate S. Typhimurium virulence. To use RNA-seq to analyze the transcriptome patterns of pat or cobB mutation in Salmonella Typhimurium 14028s.

2016-08-10 | E-GEOD-71907 | biostudies-arrayexpress

The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PAT-seq]

Project description:The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PAT-seq]

| PRJNA952206 | ENA