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TranscriptomicsNascent-seq indicates widespread cotranscriptional RNA editing in Drosophila
The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila, by isolating nascent RNA from adult fly heads and subjecting samples to high-throughput sequencing. There ...
ORGANISM(S): Drosophila melanogaster 
2012-05-31 | E-GEOD-37232 | biostudies-arrayexpress
TranscriptomicsADAR1-mediated A-to-I RNA editing is essential for erythropoiesis [RNA-seq]
Purpose: RNA editing by ADAR1 is essential for hematopoietic development. The goals of this study were firstly, to identify ADAR1-specific RNA-editing sites by indentifying A-to-I (G) RNA editing sites in wild type mice that were not edited or reduced in editing frequency in ADAR1 deficient murine e...
ORGANISM(S): Mus musculus 
2016-07-24 | E-GEOD-71042 | biostudies-arrayexpress
TranscriptomicsThe dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome
Purpose: The purpose of this experiment is to expand the repertoire of C. elegans edited transcripts and identify the roles of ADR-1 as indirect regulator of editing and ADR-2 as the only active deaminase in vivo. Methods: Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by...
ORGANISM(S): Caenorhabditis elegans 
2014-01-20 | E-GEOD-51556 | biostudies-arrayexpress
MetabolomicsMetabolic profiling of ob/ob mouse fatty liver using HR-MAS 1H-NMR combined with gene expression analysis reveals alterations in betaine metabolism and the transsulfuration pathway
Metabolic perturbations resulting from excessive hepatic fat accumulation are poorly understood. Thus, in this study, leptin-deficient ob/ob mice, a mouse model of fatty liver disease, were used to investigate metabolic alterations in more detail. Metabolites were quantified in intact liver tissues ...
2018-01-31 | MTBLS400 | MetaboLights
TranscriptomicsEvolutionary and ontogenetic changes in RNA editing in human, chimpanzee and macaque brains
we used RNA-Seq to quantify the RNA editing level at more than 8,000 previously annotated exonic A-to-I RNA editing sites in two brain regions - prefrontal cortex and cerebellum - of humans, chimpanzees and rhesus macaques. We observed substantial conservation of RNA editing levels between the brain...
ORGANISM(S): Macaca mulatta 
2014-01-07 | E-GEOD-45244 | biostudies-arrayexpress
TranscriptomicsAlu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing
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 ...
ORGANISM(S): Homo sapiens 
2010-07-29 | E-GEOD-19719 | biostudies-arrayexpress
TranscriptomicsAdenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation
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 mRN...
ORGANISM(S): Homo sapiens 
2016-09-05 | E-GEOD-60217 | biostudies-arrayexpress
TranscriptomicsRNA Sequencing Quantitative Analysis and identification of RNA editing sites of Wild Type and ADAR1 editing deficient (ADAR1E861A) murine fetal liver RNA
Purpose: RNA editing by ADAR1 is essential for hematopoietic development. The goals of this study were firstly, to identify ADAR1-specific RNA-editing sites by indentifying A-to-I (G) mismatches in RNA-seq data compared to mm9 reference genome in wild type mice that were not edited or reduced in edi...
ORGANISM(S): Mus musculus 
2015-07-23 | E-GEOD-58917 | biostudies-arrayexpress
GenomicsMiSeq paired-end sequencing of HEK293T cells stably expressing a Cas9/gRNA-dependent editable reporter vector to test novel nucleobase-editing techniques
The goal of these experiments were to test the on-target and target-adjacent editing efficiencies of different single-nucleobase editing systems. Previous studies have shown that tethering DNA mutating enzymes to Cas9-nickase-UGI complexes results in editing of chromosomal DNA. However, these editin...
ORGANISM(S): Homo sapiens 
2020-02-23 | E-MTAB-8742 | biostudies-arrayexpress
TranscriptomicsGenome-wide identification and functional analysis of Apobec-1 mediated C-to-U RNA editing in mouse small intestine and liver
The genome-wide identification, tissue-specificity and functional implications of Apobec-1 mediated C-to-U RNA editing remains incomplete. Deep sequencing, data filtering and validation from wild-type and Apobec-1 deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sit...
ORGANISM(S): Mus musculus 
2014-05-23 | E-GEOD-57910 | biostudies-arrayexpress
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