Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq

ABSTRACT: Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq

PROVIDER: PRJNA548673 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11517308.fastq.gz	Fastqsanger.gz
	SRR11517309.fastq.gz	Fastqsanger.gz
	SRR11517310_1.fastq.gz	Fastqsanger.gz
	SRR11517310_2.fastq.gz	Fastqsanger.gz
	SRR11517311_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq

Project description:We develop a method Re-Cappable-seq for determining eukaryotic transcription start sites derived from all RNA polymerases at nucleotide resolution. In particular, this method identifies the Pol-I and Pol-III TSSs, which are missing by CAGE. Applied to human A549 cell line, our method results in the identification of 33,468 and 5,269 high confidence Pol-II and non-Pol-II TSS respectively. Re-Cappable-seq identifies Pol-II TSS with higher specificity than CAGE.

2019-06-14 | GSE132660 | GEO

Determination of Transcriptional start sites in S. aureus USA300 (JE2) during exponential phase

Project description:Transcriptional start sites determination of USA300 (JE2) by using dRNA-Seq

2016-05-04 | GSE67424 | GEO

Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.

Project description:Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the other RNA polymerases that also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq, which comprehensively identifies TSS for both Pol II and non-Pol II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5' m7G caps and 5' triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol II TSSs that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSSs associated with Pol III transcripts that have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and noncoding RNA concurrently and enables the classification of epigenetic profiles associated with Pol II and non-Pol II TSS.

| S-EPMC8744680 | biostudies-literature

Determination of transcriptional start sites in the presence of GABA for Corynebacterium glutamicum

Project description:Determination of transcriptional start sites in the presence of GABA for Corynebacterium glutamicum

| PRJNA658771 | ENA

CAGE mapping Drosophila Hemocytes start sites

Project description:CAGE mapping Drosophila Hemocytes start sites

| PRJEB45705 | ENA

Analysis of Drosophila melanogaster nascent transcription start sites

Project description:Analysis of Drosophila melanogaster nascent transcription start sites

| PRJNA838629 | ENA

Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells

Project description:Background: The expression of microRNAs (miRNAs) is primarily regulated during their transcription. However, the transcriptional regulation of miRNA genes has not been studied extensively owing to the lack of sufficient information about the promoters and transcription start sites of most miRNAs. Results: In this study, we identified the transcription start sites of human primary miRNAs (pri-miRNAs) using DROSHA knockout cells. DROSHA knockout resulted in increased accumulation of pri-miRNAs and facilitated the precise mapping of their 5′ end nucleotides using the rapid amplification of cDNA ends (RACE) technique. By analyzing the promoter region encompassing the transcription start sites of miRNAs, we found that the unrelated miRNAs in their sequences have many common elements in their promoters for binding the same transcription factors. Moreover, by analyzing intronic miRNAs, we also obtained comprehensive evidence that miRNA-harboring introns are spliced more slowly than other introns. Conclusions: The precisely mapped transcription start sites of pri-miRNAs, and the list of transcription factors for pri-miRNAs regulation, will be valuable resources for future studies to understand the regulatory network of miRNAs.

2016-10-05 | GSE80258 | GEO

Profiling of alternative transcription start sites and alternative polyadenylation sites in Xenopus tropicalis

Project description:We have developed both WTSS-seq (whole transcriptome start site sequencing) and WTTS-seq (whole transcriptome termini site sequencing) methods to capture either 5’- or 3’-ends of transcripts. HATT-seq (head and tail tag sequencing) is still under development, which can be used to capture both 5’- and 3’ ends of each transcript simultaneously. Iso-seq was used to produce full-length transcripts, which can be used to validate both alternative transcription start sites and alternative polyadenylation sites. CAGE-seq was used to confirm alternative transcription start sites only.

2020-02-01 | GSE110063 | GEO

Determination of the transcription start sites of heterologous promoters in Actinoplanes sp. SE50/110 by 5'-end specific transcriptome sequencing

Project description:The promoter structure influences binding and clearance of RNA polymerase and therefore substantially influences expression of a gene. A promoter usually consists of a -10 and a -35-region, an extended -10-motif and A+T-rich upstream promoter elements. Most of these elements are optional, whereas the -10-region is essential (Albersmeier et al. 2017). Knowledge about the transcription start sites (TSS) of genes allows genome-wide localization and determination of the promoter regions. In our group, a special protocol for the amplification of primary transcripts was developed, including the capture of primary transcripts, rewriting them into cDNA (complementary DNA) and amplification in the further course of the protocol (Pfeifer-Sancar et al. 2013). Here, TSS were manually determined with special regard to the heterologous promoters. For each construct, at least one and up to three different TSS were found, leading to the identification of one or several -10-core-hexamers. These were located mostly 6 to 7 nucleotides upstream of each TSS, which corresponds to the average distance of 6.4 nt described for Actinoplanes sp. SE50/110 by Schwientek et al. (2014).

2019-10-26 | E-MTAB-8433 | biostudies-arrayexpress

BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites.

Project description:BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites.

| PRJNA853953 | ENA