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Drosophila melanogaster

ABSTRACT: Detection of circRNA in Drosophila Fly heads and S2 cells using RNA-seq with or without RNaseR tretment

PROVIDER: PRJNA241181 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1191330.fastq.gz	Fastqsanger.gz
	SRR1191340.fastq.gz	Fastqsanger.gz
	SRR1191331.fastq.gz	Fastqsanger.gz
	SRR1191332.fastq.gz	Fastqsanger.gz
	SRR1191323.fastq.gz	Fastqsanger.gz

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Detection of circRNA in Drosophila Fly heads and S2 cells using RNA-seq with or without RNaseR tretment

Project description:We determined circRNA abundance in fly Heads and S2 cells by generating and analyzing high-throughput RNA-sequencing libraries prepared from rRNA-depleted RNA. In order to determine whether the observed sequencing reads are due to bona fide circRNAs, we pre-treated the RNA with RNAse-R before the rRNA-depletion procedure. Indeed, most of the identified circRNAs were more enriched in comparison to the canonical mRNA isoforms following the RNAse-R treatment. We compare circRNA levels in wt (Canton S) flies with flies carrying the C4 ("slow polymerase") mutation. 4 samples of Drosophila Canton S and 4 samples of flies carrying the C4 ("slow polymerase") mutation. For each sample, one library was prepared from RNA after RNaseR treatment and the second from RNA with without treatment (mock). RNA library from one Canton Sample was used for stranded libray preprepation.

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Detection of circRNA in Drosophila Fly heads and S2 cells using RNA-seq with or without RNaseR tretment

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Nascent-Seq Indicates Widespread Cotranscriptional pre-mRNA Splicing in Drosophila

Project description:To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced nascent RNA transcripts from Drosophila S2 cells as well as from Drosophila heads. 87% of introns assayed manifest more than 50% cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced poorly, or slowly, with ~3% being almost completely retained in nascent pre-mRNA. Although individual introns showed slight but statistically significant differences in splicing efficiency, similar global levels of splicing were seen from both sources. Importantly, introns with low cotranscriptional splicing efficiencies are present in the same primary transcript with efficiently spliced introns, indicating that splicing is intron-specific. The analysis also indicates that cotranscriptional splicing is less efficient for first introns, longer introns and introns annotated as alternative. FinallyFinally, S2 cells expressing the slow RpII215C4 mutant manifest substantially less intron retention than wild-type S2 cells. Examination of Total pA and Nascent RNA from 2 different cell populations and isolated fly heads.

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