GEO DataSets

(Submitter supplied) Adenosine deaminases, RNA specific (ADAR) are proteins that deaminate adenosine to inosine which is then recognized in translation as guanosine. To study the roles of ADAR proteins in RNA editing and gene regulation, we carried out DNA and RNA sequencing, RNA interference and RNA-immunoprecipitation in human B-cells. We also characterized the ADAR protein complex by mass spectrometry. The results uncovered over 60,000 sites where the adenosines (A) are edited to guanosine (G) and several thousand genes whose expression levels are influenced by ADAR. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: BED, TXT

(Submitter supplied) Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

38 Samples

Download data: CSV, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL5175 GPL10999

8 Samples

Download data: CEL

(Submitter supplied) Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: XLS

(Submitter supplied) Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

4 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

23 Samples

Download data: TXT

(Submitter supplied) We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in ADAR1-3 overexpressed HEK293 cells and control HEK293 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in ADAR1-3 overexpressed HEK293 cells and control HEK293 cells

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

11 Samples

Download data: TXT

(Submitter supplied) Molecular tools to target RNA site‐specifically allow recoding of RNA information and processing. SNAP‐tagged deaminases, guided by a chemically stabilized guideRNA, enable the simultaneous editing of targeted adenosine to inosine in several endogenous transcripts, with high efficiency (up to 90%), high potency, sufficient duration, and high precision. We applied SNAP‐ADARs for the efficient and concurrent editing of two disease‐relevant signaling transcripts, KRAS and STAT1. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19132 GPL19057

66 Samples

Download data: TXT

(Submitter supplied) Zn72D is an RNA binding protein that alters A-to-I RNA editing and splicing in the fly brain. We performed RNA immunoprecipitation and sequencing (RIP-seq) to identify the RNAs that are bound by Zn72D.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

6 Samples

Download data: TXT

(Submitter supplied) We used RNA-seq of mouse primary cortical neurons transfected with control shRNAs or shRNAs targeting ADAR1, ADAR2, or Zfr to test for A-to-I RNA editing level differences between control and knockdown neurons.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT

(Submitter supplied) A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We used RNA-seq on whole fly brains with different RNA binding proteins knocked down to test for A-to-I RNA editing level differences between controls and knockdowns.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

48 Samples

Download data: TXT

(Submitter supplied) We used transgenic mouse embryos that are deficient in the two enzymatically active RNA editing enzymes ADAR1 and ADAR2 to compare relative frequencies but also sequence composition of mature miRNAs in these genetically modified backgrounds to wild-type mice by Illumina next gen sequencing. Deficiency of ADAR2 leads to a reproducible change in abundance of specific miRNAs and their predicted targets. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL13912 GPL9250

13 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

56 Samples

Download data: TXT

(Submitter supplied) A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We performed RNA-seq on M17 and HeLa cells with overexpression of different candidate Adar regulators and GFP as a control to assay editing level differences between overexpression and control.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We performed mmPCRseq on H239T and H293TAdar2OE cells with overexpression of different candidate Adar regulators and GFP as a control to assay editing level differences between overexpression and control.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

40 Samples

Download data: TXT

(Submitter supplied) Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. Using microfluidics-based multiplex PCR sequencing (mmPCR-seq) to assess A-to-I editing at 146 pre-selected, conserved sites, we found that editing was generally higher in adult compared to neonatal rat brain, and that at birth, global editing was lower in prefrontal cortex than in amygdala. more...

Organism:

Rattus norvegicus

Type:

Other

Platform:

GPL20084

85 Samples

Download data: TXT

(Submitter supplied) Conversion, or editing, of adenosine (A) into inosine (I) catalyzed by specialized cellular enzymes represents one of the most common naturally occurring post-transcriptional RNA modifications found in multiple species from fruit flies to humans with emerging connection to disease, particularly cancer. The A-to-I conversion can happen at specific sites in certain RNA molecules and lead to mRNA recoding and increase in proteome diversity, changes in RNA stability, splicing and regulation. more...

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

96 Samples

Download data: TXT

(Submitter supplied) Adenosine to Inosine (A-to-I) RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA) protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3’UTRs, 5’UTRs and introns - mainly in Alu elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

2 Samples

Download data: CEL