Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing HEK 293T cells Transcriptomes

ABSTRACT: Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing HEK 293T cells Transcriptomes

PROVIDER: PRJNA422806 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6384877_1.fastq.gz	Fastqsanger.gz
	SRR6384877_2.fastq.gz	Fastqsanger.gz
	SRR6384878_1.fastq.gz	Fastqsanger.gz
	SRR6384878_2.fastq.gz	Fastqsanger.gz
	SRR6384879_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing HEK 293T cells Transcriptomes

Project description:Purpose: A-to-I RNA editing is critical for many cellular processes. The sites of A-I RNA editing can be identified through RNA-seq and matching the reads to the annotated database like RADAR. The goals of this study is to compare A-I RNA editing profile among wild type, ADAR2 overexpressing and ADAR2+SRSF9 overexpressing 293T cells to evaluate the influence of SRSF9 repressive action on A-I RNA editing Methods: A-I RNA editing profile and gene expression profiles were generated by deep sequencing from all the samples, using NEBNext® Ultra™ Directional RNA Library Prep Kit. The sequence reads that passed quality filters were analyzed for identifying the A-I RNA editing sites using RADAR Database Results: Upon overexpression of ADAR2, we found that 18,174 sites were differentially edited compared to control cells, of which 97.0% showed a significant increase in their editing levels as expected (P < 0.05, Fisher’s test). Furthermore, when we overexpressed both ADAR2 and SRSF9 together, we found that 6,994 sites were differentially edited compared to overexpression of the deaminase alone (P < 0.05, Fisher’s test). Importantly, the editing of 92.5% of these sites was down-regulated, consistent with the function of SRSF9 as a repressor of editing. Conclusions: Our study reports a detailed analysis of the effect of SRSF9 on A-I RNA editing of ADAR2-specific targets. We Conclude that this SRSF9 regulon is significantly enriched for brain-specific editing sites despite our unbiased approach.

2018-06-21 | GSE108126 | GEO

Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing SH-Sy5y cells Transcriptomes

2018-06-21 | GSE114970 | GEO

Transcriptome-wide map of SRSF9 bining in the presence and absence of ADAR2 in HEK293T cells

Project description:Here, we show that the splicing factor SRSF9 selectively controls the editing of many brain-specific sites in mammals. SRSF9 is more lowly expressed in the mammalian brain than in non-brain tissues. Gene perturbation experiments and minigene analysis of candidate sites demonstrated that SRSF9 could robustly repress A-to-I editing by ADAR2. We found that SRSF9 biochemically interacted with ADAR2 in the nucleus via its RRM2 domain alone. Additionally, this interaction required the presence of the RNA substrate and disrupted the formation of ADAR2 dimers. Using transcriptome-wide location analysis and genome-wide RNA profiling, we identified 1,328 editing sites that are regulated directly by SRSF9. Importantly, we showed that this SRSF9 regulon is significantly enriched for brain-specific editing sites despite our unbiased approach. We further provide evidence that SRSF9 prevents cells from undergoing apoptosis possibly through the inhibition of ADAR2-mediated editing. Collectively, our results highlighted the importance of SRSF9 as an editing regulator and suggested that other splicing factors may also be involved in regulating RNA editing.

2018-06-21 | GSE108125 | GEO

Tumorigenic effects of TLX over-expression in HEK 293T cells

Project description:Transcriptomic profiling to investigate the effect of TLX overexpression with an inducible vector system in the HEK 293T cell line

2021-01-21 | GSE120893 | GEO

Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing SH-Sy5y cells Transcriptomes

Project description:Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing SH-Sy5y cells Transcriptomes

| PRJNA473370 | ENA

nsp1 acts on HEK-293T

Project description:nsp1 acts on HEK-293T

| PRJNA600748 | ENA

Effect of depletion of C17orf80 on mtDNA transcription in HEK-293T cells

Project description:Effect of depletion of C17orf80 on mtDNA transcription in HEK-293T cells

2023-09-02 | GSE224121 | GEO

DNA methylation profiling for HEK-293T cells transfected with GFP and DMEΔ

Project description:Methylome data obtained from human embryonic kindey (HEK)-293T cells expressing a GFP (293T-GFP) or a truncated form of Arabidopsis DEMETER (DME) 5-methylcytosine (5mC) DNA glycosylase (293T-DMEΔ) analyzed on a Human Methylation 450K BeadChip platform (Illumina). These methylation array data revealed genome-wide DNA methylation patterns of the 293T-GFP cells (without direct 5mC excision activity) and 293T-DMEΔ cells (with artificially implemented direct 5mC excision activity).

2017-09-20 | GSE96864 | GEO

ASFV I73R acts on HEK-293T

Project description:ASFV I73R acts on HEK-293T

| PRJNA782452 | ENA

Role of BACH1 in HEK 293T cells

Project description:This SuperSeries is composed of the following subset Series: GSE28050: Expression data from knockdown of BACH1 in HEK 293T cells GSE28051: Genome-wide map of BACH1 binding in HEK293T cells Refer to individual Series

2011-05-12 | E-GEOD-28053 | biostudies-arrayexpress

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