Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-MTAB-2456

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

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

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-MTAB-2456-analysis-methods.tsv	Tabular
	E-MTAB-2456-analytics.tsv	Tabular
	E-MTAB-2456-analytics.tsv.rounded	Tabular
	E-MTAB-2456-analytics.tsv.undecorated	Tabular
	E-MTAB-2456-analytics.tsv.undecorated.rounded	Tabular

Items per page:

1 - 5 of 1796

Similar Datasets

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

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

| PRJEB6043 | ENA

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

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

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [human K562 and muring 3T3]

Project description:While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. This approach enables robust cell-typing of complex tissues and reveals a de novo atlas of cellular and epigenomic diversity across many cell types and cell stages.

2019-05-02 | GSE130536 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Bone marrow]

2019-05-02 | GSE123580 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [species mixture]

2019-05-02 | GSE123579 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Blood]

2019-05-02 | GSE123578 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [PBMC]

2019-05-02 | GSE123577 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [GM12878]

2019-05-02 | GSE130537 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Validation]