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| Status |
Public on Aug 09, 2019 |
| Title |
The transcriptome of larval carcasses from both wildtype and Nxt1 trans-heterozygotes |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
The transcriptome of larval carcasses from both wildtype and Nxt1 trans-heterozygotes were assessed by RNA-Seq. A total of 1821 genes were down-regulated and 1339 genes were up-regulated. Down-regulated genes had a higher total intron length and had more introns, while up-regulated genes had a lower total intron length and less introns when compared to the non-differentially expressed genes. The majority of down-regulated genes were involved in the production of circular RNAs (circRNAS). We further investigated circRNA expression in larval carcasses from both wildtype and Nxt1 trans-heterozygotes by sequencing total RNA after RNAseR treatment. RNAseR digests linear RNA and thus enriches for circRNAs. Mock samples without RNAseR treatment were also sequenced. We found that circRNA products of Nxt1-responsive genes are reduced in Nxt1 mutants, although the nascent transcripts of these genes are produced at normal levels.
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| Overall design |
To assess the effect of Nxt1 on circRNA expression, we sequenced and analysed total RNA with and without RNAseR treatment from Nxt1 trans-heterozygotes and wildtype larval carcasses. All samples were sequenced in triplicates. We analysed pre-mRNA:mRNA:circRNA ratios, as well as the different CircRNA structures formed.
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| Contributor(s) |
Jindrich K, White-Cooper H |
| Citation missing |
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| Submission date |
Aug 08, 2019 |
| Last update date |
Aug 11, 2019 |
| Contact name |
Helen White-Cooper |
| E-mail(s) |
White-CooperH@cardiff.ac.uk
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| Organization name |
Cardiff University
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| Department |
School of Biosciences
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| Street address |
Museum Avenue
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| City |
Cardiff |
| State/province |
Wales |
| ZIP/Postal code |
CF10 3AX |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA559379 |
| SRA |
SRP217856 |
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