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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
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
ProteomicsProximity labeling on phosphatidic acid-enriched membranes generated via optogenetic membrane editing
Cellular lipid metabolism is subject to strong homeostatic regulation, but players involved in and mechanisms underlying these pathways remain mostly uncharacterized. Here, we develop and exploit a “Feeding-Fishing” approach coupling membrane editing using optogenetic lipid-modifying enzymes (feedin...
ORGANISM(S): Homo sapiens (Human) 
2026-02-23 | PXD070378 | Pride
Feeding-fishing Membrane-turboid Optopld Membrane editing Phospholipase d Phosphatidic acid 
ProteomicsProximity labeling on phosphatidic acid-enriched membranes generated via optogenetic membrane editing (set2)
Cellular lipid metabolism is subject to strong homeostatic regulation, but players involved in and mechanisms underlying these pathways remain mostly uncharacterized. Here, we develop and exploit a “Feeding-Fishing” approach coupling membrane editing using optogenetic lipid-modifying enzymes (feedin...
ORGANISM(S): Homo sapiens (Human) 
2026-02-23 | PXD070270 | Pride
Feeding-fishing Membrane-turboid Optopld Membrane editing Phospholipase d Phosphatidic acid 
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
TranscriptomicsRNA-Seq of human hematopoietic stem and progenitor cells to study membrane repair following electroporation (EP) or filtroporation (FP) disruption based strategies for intracellular delivery
This experiment investigates how different intracellular delivery methods, specifically filtroporation (FP) and electroporation (EP) affect gene editing efficiency and cellular responses in human hematopoietic stem and progenitor cells. By comparing these methods, results show how mechanical versus ...
ORGANISM(S): Homo sapiens 
2025-10-30 | E-MTAB-15741 | biostudies-arrayexpress
TranscriptomicsRNA-seq of 9 tissues from an adult male C57BL/6 mouse
RNA-editing is a tightly regulated, and essential cellular process for a properly functioning brain. Dysfunction of A-to-I RNA editing can have catastrophic effects, particularly in the central nervous system. Thus, understanding how the process of RNA-editing is regulated has important implications...
ORGANISM(S): Mus musculus 
2016-01-19 | E-GEOD-74747 | biostudies-arrayexpress
ProteomicsA-to-I mRNA editing controls disulfide bond formation and the toxicity of the HokB toxin in bacteria
Protein disulfide bonds between cysteine residues serve a prominent role in bacterial protein function, virulence, and viability. Adenosine-to-inosine (A-to-I) mRNA editing changes the genetic information at the RNA level. Previously, we discovered that A-to-I mRNA editing occurs in bacteria (Escher...
ORGANISM(S): Escherichia coli 
2025-07-14 | PXD051162 | Pride
Tada Adenosine-to-inosine rna editing Toxin-antitoxin Disulfide bond Hokb Bacteria Dsba 
TranscriptomicsGenome-wide chromatin binding analysis (ChIP-seq) of HA epitope tagged RFX6 protein in human embryonic stem cell derived pancreatic progenitors
To identify direct transcriptional targets of RFX6, we performed chromatin immunoprecipitation of HA epitope tagged RFX6 followed by massively parallel DNA sequencing (ChIP-seq). Using CRISPR/Cas9 gene editing, the HA epitope was inserted into the 3' end of the RFX6 gene in H9 hESC. Pluripotent cell...
ORGANISM(S): Homo sapiens 
2020-10-23 | E-MTAB-9335 | biostudies-arrayexpress
TranscriptomicsDifferential gene expression in mutants of Arabidopsis FAX1 compared to wild type
DNA microarray analysis (Affymetrix ATH1 GeneChip) on mutant lines of the gene At-FAX1 (At3g57280) in Arabidopsis thaliana was performed as described in Li et al. (2015). In total we analyzed the following comparisons: (A) flowers: fax1 knockout (n = 5) versus wild type (n = 5); (B) flowers: FAX1 ov...
ORGANISM(S): Arabidopsis thaliana 
2015-02-04 | E-MTAB-3090 | biostudies-arrayexpress
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