Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of transcripts whose abundance changes in response to acute switches in DSX isoform

ABSTRACT: RNAseq of dissected adult fat body after DSX isoform is switched using temperature inducible alleles or constructs. Biological duplicates were sequenced for each genotype at each condition.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Brian Oliver

PROVIDER: E-GEOD-55848 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of transcripts whose abundance changes in response to acute switches in DSX isoform in the ovary and testis

Project description:RNAseq of dissected adult ovary and testis after DSX isoform is switched using temperature inducible alleles or constructs. Biological duplicates were sequenced for each genotype at each condition.

2016-03-17 | E-GEOD-79294 | biostudies-arrayexpress

Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED

Project description:Neuroendocrine (NE) cells use large dense core vesicles (LDCVs) to traffic, process, store and secrete neuropeptide hormones through the regulated secretory pathway. The DIMM basic helix-loop-helix transcription factor of Drosophila controls the level of regulated secretory activity in NE cells. To pursue its mechanisms, we have performed two independent genome-wide analyses of DIMMM-bM-^@M-^Ys activities: (i) in vivo chromatin immunoprecipitation (ChIP) to define genomic sites of DIMM occupancy and (ii) deep sequencing of purified DIMM neurons to characterize their transcriptional profile. By this combined approach, we showed that DIMM binds to conserved E-boxes in enhancers of 212 genes whose expression is enriched in DIMM-expressing NE cells. DIMM binds preferentially to certain E-boxes within first introns of specific gene isoforms. Statistical machine learning revealed that flanking regions of putative DIMM binding sites contribute to its DNA binding specificity. DIMMM-bM-^@M-^Ys transcriptional repertoire features at least 20 LDCV constituents. In addition, DIMM notably targets the pro-secretory transcription factor, CREB-A, but significantly, DIMM does not target any neuropeptide genes. DIMM therefore prescribes the scale of secretory activity in NE neurons, by a systematic control of the regulated secretory pathway at steps that are both proximal and distal. DIMM::MYC ChIP-chip (c929>DIMM::MYC/tubGAL80ts) and control (c929>tubGAL80ts): 2 replicates each, input and IP samples. Total of 8 arrays

2015-02-02 | E-GEOD-65512 | biostudies-arrayexpress

Transcriptional profiling of Drosophila wing pouch following CR32027 RNAi

Project description:The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation. Two RNAi lines of CR32027, a non-coding RNA gene identified in this study, are examined for transcriptional changes relative to wt. Transcriptional profiles of two RNAi knockdowns, CR32027-IR1 and CR32027-IR2, are examined in Drosophila wing pouch relative to OreR wt in triplicate by RNA Seq.

2014-03-15 | E-GEOD-54927 | biostudies-arrayexpress

Transcription profiling of Drosophila adults to assess the effect of LARK overexpression in CNS neurons

Project description:The goal of this study is to identify, in the head of adult flies, mRNA species whose expresson level are altered by overexpression of the Drosophila RNA-binding protein LARK in CNS neurons. Experiment Overall Design: RNA samples from adult head of the LARK overexpression flies (elav-gal4; uas-lark/+) and control flies were compared. One total RNA sample was isolated from each genotype, of which three technical replicates (repeating the labeling and hybridization processes) were generated, respectively.

2008-06-14 | E-GEOD-6420 | biostudies-arrayexpress

Identifying targets of DSX with DamID-seq

Project description:We have adapted the DamID protocol for use with high throughput sequencing. We have used DamID to identify the positions within the Drosophila genome where the transcription factor DSX is bound. We sequenced DpnI-digested genomic DNA from fly tissues containing UAS-Dam (control) or UAS-Dam-DsxF or UAS-Dam-DsxM. We have performed DamID-seq on adult male and female fatbody and on ovary. We used two biological replicates for each tissue and sex.

2014-10-30 | E-GEOD-27269 | biostudies-arrayexpress

The SWI/SNF Complex Regulates the PRDM Protein Hamlet to Ensure Lineage Directionality in Drosophila Neural Stem Cells

Project description:Members of the SWI/SNF chromatin-remodeling complex are among the most frequently mutated genes in human cancer. SWI/SNF complex controls self-renewal and differentiation in stem cell lineages but how this function relates to tumorigenesis is currently unclear. Here, we use Drosophila neuroblasts to demonstrate that the SWI/SNF component Osa (ARID1) prevents tumorigenesis in stem cell lineages by ensuring correct unidirectional lineage progression. Our transcriptome anaysis identifies Ham as a key Osa target gene. comparison of transcriptomes of wild type Drosophila melanogaster larval type II NB lineages (excluding neurons) and osa RNAi type II lineages containing mainly NB-like cells and INPs

2014-03-13 | E-GEOD-48242 | biostudies-arrayexpress

RNA-seq on Drosophila wing imaginal discs after Myc RNAi or overexpression

Project description:RNA-seq was performed to confirm the effect of dMyc overexpression or RNAi repression on conserved Myc targets in the Drosophila wing disc.

2022-04-26 | E-MTAB-9328 | biostudies-arrayexpress

Dm Ladybird over-expression and loss-of-function Expression Profiling

Project description:In order to identify Ladybird mesodermal and heart target genes, we decided to analyse the transcriptional profiling of embryos with a targeted gain and Loss of function approach. Embryos were collected at stages 11 to 15 of embryogenesis corresponding to the lb expression period. Homozygous ectopically expressing or repressing embryos were collected from a large scale cross of UAS-lbe or UAS-RNAi-lbe flies with 24B-Gal4 or Tin-Gal4 flies, in parallel to stage-matched control. Three independent collections were performed. Total RNA was extracted. Ectopically expression and reference samples were hybridized together on GeneChip Drosophila Genome array2. With this approach, we were able to dicover a repertory of genes involved in different aspects of muscle and heart formation showing a multi-step action of this family of identity genes.

2008-02-05 | E-TABM-297 | biostudies-arrayexpress

fly brm knockdown RNA-seq

Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted next-generation sequencing (NGS) to analyse the expression profile in both control and Brm knockdown fly larvae.

2014-05-08 | E-MTAB-1966 | biostudies-arrayexpress

Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-03-15 | E-GEOD-54928 | biostudies-arrayexpress