Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The transcriptome of larval carcasses from both wildtype and Nxt1 trans-heterozygotes

ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE135591 | GEO | 2019/08/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in larval carcasses

Project description:We used larval carcasses of both wildtype and Nxt1 trans-heterozygotes for RNA paired-end sequencing and obtained a read depth between 21M to 32M reads across all samples. A total of 1821 genes were down-regulated and 1339 genes were up-regulated. A python script extracting intron data of genes from the FlyMine database identified a trend where down-regulated genes had a higher total intron length and had more introns. Up-regulated genes had a lower total intron length and less introns when compared to the non-differentially expressed genes. Furthermore, down-regulated genes showed that the majority of genes are involved in the production of circular RNAs

2019-01-29 | GSE125776 | GEO

The transcriptome of larval carcasses from both wildtype and Nxt1 trans-heterozygotes

Project description:The transcriptome of larval carcasses from both wildtype and Nxt1 trans-heterozygotes

| PRJNA559379 | ENA

Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in larval carcasses

Project description:Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in larval carcasses

| PRJNA517487 | ENA

Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in whole larvae

Project description:We used whole larvae of both wildtype and Nxt1 trans-heterozygotes for RNA paired-end sequencing and obtained a read depth between 6.4M to 11.1M reads across all samples. In wandering larvae, stationary larvae and white prepupae, a total of 435, 855, and 611 genes were differentially expressed. A high percentage of down-regulated genes were highly expressed/testis-specific in the Drosophila testis.

2019-01-29 | GSE125781 | GEO

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals

Project description:Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. By scoring the presence of reverse complementary sequences in human introns we predicted and experimentally validated novel circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyper-editing events. Knockdown of the double-strand RNA editing ADAR1 enzyme significantly and specifically up-regulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA:RNA interactions of introns form larger structures which promote circularization of embedded exons, while ADAR1 antagonizes circRNA expression by melting stems within these interactions. Thus, we assign a new function to ADAR1. Examination of 12 samples in different stages of C.elegans development.

2015-01-06 | E-GEOD-63823 | biostudies-arrayexpress

Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation II

Project description:M17 and HOG cells were induced differentiation and subject to A-tailing RNaseR treatment, circRNA were identified by rRNA depleted RNA-seq data from A-tailing RNaseR and untreated samples

2022-02-14 | GSE181636 | GEO

Drosophila U6atac snRNA mutant

2010-10-11 | GSE24148 | GEO

Drosophila U6atac snRNA mutant

Project description:A Drosophila line (l(2)k01105) with a P-element insertion in U6atac snRNA, an essential component of the U12-type spliceosome, was used to investigate the impact of disrupted U12-dependent splicing during larval development. A custom-designed exon array was used to study the expression of genes containing U12-type introns and genes involved in downstream pathways affected by deficient U12-dependent splicing. Flies homozygous for the U6atac mutation (U6atac/U6atac) were compared to heterozygotes (U6atac/CyO-GFP) which have a normal phenotype. Samples from homozygous and heterozygous U6atac mutant larvae at 1st, 2nd and 3rd larval instar were labelled with three colours and hybridized three samples per array. Three independently harvested biological replicates were made, with dye swap, except only two replicates for 3rd stage heterozygous control. This study presents exon-level data. Supplementary files: Raw data (.gpr) files. Series variables and repeats information.

2010-10-11 | E-GEOD-24148 | biostudies-arrayexpress

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals

2015-01-06 | GSE63823 | GEO

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.

2014-10-14 | E-GEOD-55872 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data