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Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

ABSTRACT: Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

PROVIDER: PRJNA453551 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7063210.fastq.gz	Fastqsanger.gz
	SRR7063220.fastq.gz	Fastqsanger.gz
	SRR7063230.fastq.gz	Fastqsanger.gz
	SRR7063211.fastq.gz	Fastqsanger.gz
	SRR7063221.fastq.gz	Fastqsanger.gz

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Measuring A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

Project description:Measuring A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

| PRJNA453552 | ENA

Measuring A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

Project description:We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using microfluidic multiplex PCR and sequencing (mmPCR-seq), we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control.

2019-01-18 | GSE113662 | GEO

Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

Project description:We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using RNA-seq, we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control.

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A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

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A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

Project description:This SuperSeries is composed of the SubSeries listed below.

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Measuring RNA editing through mmPCR-seq in Drosophila adapting to divergent microclimates and raised at different temperatures

Project description:We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) to quantify RNA editing levels at targeted sites in 32 isofemale lines from two divergent microclimates at 'Evolution Canyon' in Israel (16 fly lines from each microclimate). Editing levels were compared between different populations at 25˚C , and were also compared between 25˚C and 18˚C within populations.

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Neuronal DNA repair reveals strategies to influence CRISPR editing outcomes

Project description:Genome editing is poised to revolutionize treatment of genetic diseases, but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons, which must withstand decades of DNA damage without replicating. This lack of knowledge limits the efficiency and precision of genome editing in clinically relevant cells. To address this, we used induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. We discovered that neurons can take weeks to fully resolve this damage, compared to just days in isogenic iPSCs. Furthermore, Cas9-treated neurons upregulated unexpected DNA repair genes, including factors canonically associated with replication. Manipulating this response with chemical or genetic perturbations allowed us to direct neuronal repair toward desired editing outcomes. By studying DNA repair in postmitotic human cells, we uncovered unforeseen challenges and opportunities for precise therapeutic editing.

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Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing

Project description: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 3âUTRs, 5âUTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs). We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, our data suggest that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions. Two samples, One control and the second treated

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Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila

Project description: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 are a large number of edited sites within nascent exons. Nascent RNA from an ADAR null mutant strain was also sequenced, indicating that almost all A-to-I events require ADAR. Moreover, mRNA editing levels correlate with editing levels within the cognate nascent RNA sequence, indicating that the extent of editing is set cotranscriptionally. Surprisingly, the nascent data also identify an excess of intronic over exonic editing sites. These intronic sites occur preferentially within introns that are poorly spliced cotranscriptionally, suggesting a link between editing and splicing. We conclude that ADAR-mediated editing is more widespread than previously indicated and largely occurs cotranscriptionally. GSM914095: Fly genomic DNA sequencing. Sequenced on the Illumina GA II. GSM914102-GSM914113: Fly head nascent RNA profiles over 6 time points of a 12hr light:dark cycle in duplicate; sequenced on the Illumina GA II. GSM914114-GSM914119: Fly head nascent RNA profiles of yw, FM7, ADAR0 males in duplicate; sequenced on the HiSeq2000. GSM915213-GSM915214: Fly head mRNA profiles over 2 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II. GSM915215-GSM915220: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; paired-end sequenced on the Illumina GA II. GSM915221-GSM91526: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II.

2012-05-31 | E-GEOD-37232 | biostudies-arrayexpress

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