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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Fly brm knockdown RNA-seq

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Jiejun Shi

PROVIDER: E-MTAB-1966 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Drosophila Brahma complex remodels nucleosome organizations in multiple aspects.

Shi Jiejun J Zheng Meizhu M Ye Youqiong Y Li Min M Chen Xiaolong X Hu Xinjie X Sun Jin J Zhang Xiaobai X Jiang Cizhong C

Nucleic acids research 20140731 15

ATP-dependent chromatin remodeling complexes regulate nucleosome organizations. In Drosophila, gene Brm encodes the core Brahma complex, the ATPase subunit of SWI/SNF class of chromatin remodelers. Its role in modulating the nucleosome landscape in vivo is unclear. In this study, we knocked down Brm in Drosophila third instar larvae to explore the changes in nucleosome profiles and global gene transcription. The results show that Brm knockdown leads to nucleosome occupancy changes throughout the ...[more]

PMID: 25081211

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fly brm knockdown MNase-seq

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

2014-05-08 | E-MTAB-1967 | biostudies-arrayexpress

Transcription profiling of Drosophila tissue expressing phosphatase mutant eya shows that reducing phosphatase activity did not globally impair transcriptional output

Project description:Drosophila eye specification an development relies on a collection of transcription factors termed the retinal determination gene network (RDGN). Two members of this network, Eyes absent (EYA) and Sine oculis (SO), form a transcriptional complex in which EYA provides the transactivation function while SO provides the DNA binding activity. EYA also function as a protein tyrosine phosphatase, raising the question of whether transcriptional output is dependent or independent of phosphatase activity. To explore this, we used microarrays together with binding site analysis, quantitative real-time PCR, chromatin immunoprecipitation, genetics, and in vivo expression analysis to identify new EYA-SO targets. In parallel, we examined the expression profiles of tissue expressing phosphatase mutant eya and found that reducing phosphatase activity did not globally impair transcriptional output. Among the targets identified by our analysis was the cell cycle regulatory gene, string (stg), suggesting that EYA and SO may influence cell proliferation through transcriptional regulation of stg. Future investigation into the regulation of stg and other EYA-SO targets identified in this study will help elucidate the transcriptional circuitries whereby output from the RDGN integrates with other signaling inputs to coordinate retinal development. Experiment Overall Design: We compared gene expression across duplicate samples for controls in which eya was not overexpressed to duplicate samples in which a wildtye overexpressed eya transgene, an eya mutant transgene with the D493N mutation, which reduces phosphatase activity, and a second eya mutant transgene with the E728Q mutation, which has little is any posphatase activity.

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Transcription profiling of Drosophila transformed with two Plasmodium cell surface antigens

Project description:Two Plasmodium cell surface antigens were transformed into Drosophila, un-induced flies were compared to induced flies.

2008-12-31 | E-MEXP-1859 | 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.

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2007-10-11 | E-TABM-251 | 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

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