GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19132 GPL17275

112 Samples

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(Submitter supplied) Adult female Drosophila melanogaster flies from the w1118 background were fed sucrose, Pseudomonas entomophila (Pe), or Erwinia carotovora carotovora 15 (Ecc15).

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

12 Samples

Download data: TXT

(Submitter supplied) The lark gene was either overexpressed or silenced in adult enterocytes. Flies were fed sucrose or Pseudomonas entomophila (Pe).

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

18 Samples

Download data: TXT

(Submitter supplied) In order to gain insight into gene regulation in the Drosophila gut following oral infection, we performed the genome-wide DNA Polymerase II binding data for Polymerase II in the fly gut.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

6 Samples

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(Submitter supplied) In order to gain insights into gut immunocompetence and its variation in a population, we performed RNA-sequencing of whole guts of 38 Drosophila Genetic Reference Panel strains.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

76 Samples

Download data: TXT

(Submitter supplied) RNA-seq was used to analyze mRNA levels and splicing differences between wild-type (Oregon R) and Smn null mutant larvae.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL13304

4 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) This project uses pooled poly A (+) RNA from the DGRP to derive transcript models specific to DGRP. The derived transcript models provide the basis for quantifying gene expression in the DGRP lines using genome tiling arrays.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: GTF, TAB

(Submitter supplied) Gut immunocompetence involves immune, stress, and regenerative processes. To investigate the determinants underlying inter-individual variation in gut immunocompetence, we perform enteric infection of 140 Drosophila lines with the entomopathogenic bacterium Pseudomonas entomophila and observe extensive variation in survival. Using genome-wide association analysis, we identify several novel immune modulators. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

16 Samples

Download data: TXT

(Submitter supplied) Background: Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci -- sQTLs). Genetic variants that affect mRNA splicing in trans are harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

8 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

11 Samples

Download data: BEDGRAPH

(Submitter supplied) Methylation of mRNA at the N6 position of adenosin is known for a long time, but its function remains poorly understood. Here generated a null mutant in the catalytic subunit of the m6A mRNA methylosome, dIME4, in Drosophila to determine the impact of loss of m6A on gene expression using Illumina sequencing.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Methylation of mRNA at the N6 position of adenosin is known for a long time, but its function remains poorly understood. Here generated a null mutant in the catalytic subunit of the m6A mRNA methylosome, dIME4, in Drosophila to determine the impact of loss of m6A on gene expression using Illumina sequencing.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

5 Samples

Download data: BEDGRAPH

(Submitter supplied) The goal was to study the effects of lead exposure on gene expression and identify the lead-responsive genes. After detecting 1,536 cis-eQTLs (FDR ≤ 10%) and 952 trans-eQTLs, we focused our analysis on Pb-sensitive “trans-eQTL hotspots”.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

158 Samples

Download data: TXT

(Submitter supplied) Widespread co-transcriptional splicing has been demonstrated from yeast to human. However, measuring the kinetics of splicing relative to transcription has been hampered by technical challenges. Here, we took advantage of native elongating transcript sequencing (NET-seq) to identify the position of RNA polymerase II (Pol II) when exons become ligated in the newly synthesized RNA. We analyzed Drosophila melanogaster embryos because the genes transcribed initially during development have few and short introns (like yeast genes), whereas genes transcribed later contain multiple long introns (more similar to human genes). more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL23702

6 Samples

Download data: BED, BW

(Submitter supplied) Splicing of pre-mRNAs results in the deposition of the exon junction complex (EJC) upstream of exon-exon boundaries. The EJC plays crucial post-splicing roles in export, translation, localization and nonsense-mediated decay of mRNAs. It also aids faithful splicing of pre-mRNAs containing large introns, albeit via an unknown mechanism. Here, we show that the core EJC plus the accessory factors RnpS1 and Acinus aid in definition and efficient splicing of neighboring introns. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

9 Samples

Download data: BW, TXT

(Submitter supplied) Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. Here we address the role of the evolutionary conserved splicing co-factor Barricade (Barc)/CUS2/Tat-SF1 in Drosophila neural stem cell (neuroblast) lineage formation. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17275 GPL13304

12 Samples

Download data: TXT

(Submitter supplied) Human genes have numerous exons that are differentially spliced within pre-mRNA. Understanding how multiple splicing events are coordinated across nascent transcripts requires quantitative analyses of transient RNA processing events in living cells. We developed nanopore analysis of CO-transcriptional Processing (nano-COP), in which nascent RNAs are directly sequenced through nanopores, exposing the dynamics and patterns of RNA splicing without biases introduced by amplification. more...

Organism:

Homo sapiens; Drosophila melanogaster; synthetic construct

Type:

Expression profiling by high throughput sequencing

5 related Platforms

32 Samples

Download data: TXT

(Submitter supplied) RNA sequencing was used to identify alternative splicing events and differentially expressed genes (DEG) in 35S:HIN1 stable transgenic line compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hours moderate severity low water potential (-0.7 MPa) treatment. RNA sequencing analysis found that overexpression of HIN1 in unstressed plants was sufficient to duplicate the effects of stress on nearly 40% of the genes where intron retention was normally suppressed by stress in wild type. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: CSV, TXT

(Submitter supplied) Signaling pathways are controlled by a vast array of post-translational mechanisms. By contrast, little is known regarding the mechanisms that regulate the expression of their core components. We conducted an RNAi screen in Drosophila for factors modulating RAS/MAPK signaling and identified the Exon Junction Complex (EJC) as a novel key element of this pathway. The EJC binds the exon-exon junctions of mRNAs, and thus far, has been linked exclusively to post-splicing events. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10942

6 Samples

Download data: BAM, TXT, WIG

(Submitter supplied) The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls axon projection, locomotion, and memory. Here we define an unexpectedly specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and link the most prominent of these, female retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl), to a role in m6A-dependent mRNA splicing. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

12 Samples

Download data: TXT