Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CLT-seq as a universal homopolymer-sequencing concept reveals poly(A) tail-tuned ncRNA regulation

ABSTRACT: CLT-seq as a universal homopolymer-sequencing concept reveals poly(A) tail-tuned ncRNA regulation

PROVIDER: PRJNA835141 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19087589_1.fastq.gz	Fastqsanger.gz
	SRR19087589_2.fastq.gz	Fastqsanger.gz
	SRR19087590_1.fastq.gz	Fastqsanger.gz
	SRR19087590_2.fastq.gz	Fastqsanger.gz
	SRR19087591_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

CLT-seq as a universal homopolymer-sequencing concept reveals poly(A) tail-tuned ncRNA regulation

Project description:To more understand the poly(A) tail-tuned regulation in eukaryotic cells, we describe central limit theorem (CLT)-managed RNA-seq (CLT-seq) as a universal homopolymer-sequencing concept that features unbiased RNA-seq and facilitates accurate homopolymer base-calling. We then performed transcriptome-wide poly(A)-tail profiling analysis using data obtained from oligo(dT)-primed RNA-seq of HEK293T and A549 cell lines.

2022-05-09 | GSE202256 | GEO

Project description:CLT-seq as a universal homopolymer-sequencing concept reveals poly(A) tail-tuned ncRNA regulation

| PRJNA826542 | ENA

Discovery of RUF6 ncRNA interacting proteins involved in P. falciparum immune evasion

Project description:RUF6 is a ncRNA gene family that is transcribed by RNA Polymerase III but actively regulates the Pol II-transcribed var virulence gene family. Understanding how RUF6 ncRNA connect to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including. Affinity purification of Pf-DDX5 identified proteins originally found by our RUF6-ChIRP protocol, validating the technique’s robustness for identifying ncRNA interactomes in P. falciparum. Our work identifies a RUF6 ncRNA protein complex that interacts with RNA Pol II to sustain var gene expression.

2022-11-15 | PXD036801 | Pride

Coffea canephora ncRNA Seq

Project description:Coffea canephora ncRNA Seq

| PRJEB29660 | ENA

P-TEFb function in ncRNA transcription

Project description:Many ncRNAs serve as regulatory molecules in various physiological pathways. Distinct from protein-coding RNA expression, ncRNA expression is regulated solely by transcription and RNA processing/stability. Transcriptional regulation in ncRNA genes is thus important to be understood and is yet to be known completely. Previously, we identified that a subset of mammalian ncRNA genes is transcriptionally regulated by RNA Pol II promoter-proximal pausing and in a tissue-specific manner. In this study, human stimulus-inducible ncRNA genes were monitored to assess the function of P-TEFb, a master Pol II pausing regulator for protein-coding genes, in ncRNA transcription. Our findings indicate that the expression of many ncRNA genes is regulated by P-TEFb. Interestingly, a biphasic characteristic of P-TEFb inhibition in serum responsive ncRNA genes was observed: S2 phospho-Pol II was largely increased in the TSS (–300 to +300) whereas overall, it was decreased in the gene body (> +350) upon chemical inhibition of P-TEFb. In addition, the three representative ncRNAs, MALAT1, NEAT1, and XIST, were further analyzed for determining P-TEFb association. Taken together, we propose the transcriptional activation of many human ncRNAs utilizing pausing and releasing Pol II and the regulatory mechanism of transcriptional elongation of these genes requiring the function of P-TEFb.

2018-07-31 | GSE117848 | GEO

ncRNA termination in Saccharomyces cerevisiae

Project description:ncRNA termination in Saccharomyces cerevisiae

| PRJEB4393 | ENA

Wilms tumor versus Stratagene Universal Reference

Project description:Gene expression comparison of Wilms tumor RNA versus Stratagene Universal reference RNA Keywords: repeat sample

2004-12-31 | GSE1158 | GEO

ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification

Project description:ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification

2010-07-15 | E-MTAB-305 | biostudies-arrayexpress

poly(UG)-tailed RNAs in Genome Protection and Epigenetic Inheritance [ncRNA-Seq]

Project description:poly(UG)-tailed RNAs in Genome Protection and Epigenetic Inheritance [ncRNA-Seq]

| PRJNA623003 | ENA

Hypoxia-induced ncRNA transcriptome in TNBC cells

Project description:Whole transcriptome sequencing was performed to identify ncRNA transcriptome in two human TNBC cell lines under normoxia and hypoxia

2021-06-17 | GSE144569 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data