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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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DNA-Seq of DrosDel deficiency lines and w1118 lines

ABSTRACT: DNASeq reads from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies). Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_DNASeq_biological replicate #. We sequenced DNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies).

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Brian Oliver

PROVIDER: E-GEOD-31550 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Mediation of Drosophila autosomal dosage effects and compensation by network interactions.

Malone John H JH Cho Dong-Yeon DY Mattiuzzo Nicolas R NR Artieri Carlo G CG Jiang Lichun L Dale Ryan K RK Smith Harold E HE McDaniel Jennifer J Munro Sarah S Salit Marc M Andrews Justen J Przytycka Teresa M TM Oliver Brian B

Genome biology 20120424 4

<h4>Background</h4>Gene dosage change is a mild perturbation that is a valuable tool for pathway reconstruction in Drosophila. While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering in expression networks.<h4>Results</h4>We profiled expression in engineered flies where gene dose was reduced from two to one. While expression of most one-dose genes was ...[more]

PMID: 22531030

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Drosophila DrosDel deficiency and diploid control flies

Project description:GSE31386: Microarray expression analysis of Drosophila DrosDel deficiency lines GSE31401:RNA-Seq on SOLiD platform of DrosDel deficiency and w1118 flies GSE31549: RNA-Seq on Illumnia platform of DrosDel deficiency and w1118 lines GSE31550: DNA-Seq of Drosophila DrosDel deficiency and w1118 lines Refer to individual Series

2012-04-02 | E-GEOD-31407 | biostudies-arrayexpress

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Project description:RNA-Seq reads of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Illumina platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #_platform. We sequenced mRNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies).

2012-04-03 | E-GEOD-31549 | biostudies-arrayexpress

The Function of Piwi is Independent of Its Slicer Activity

Project description:In diverse organisms, the highly-conserved Piwi proteins bind to a complex class of small non-coding RNAs called piRNAs, and are essential for germline stem cell maintenance, transposon silencing, fertility, and offspring viability1. By homology with other Argonautes, Piwi proteins have been proposed and later reported to possess endonuclease activity in vitro, effected by its conserved aspartate catalytic triad2,3. Indeed, mutation of these residues in one of the three mouse PIWI proteins, MILI, affects the production of Line 1 piRNAs and spermatogenesis4. In Drosophila, the conserved slicer function has been proposed to be crucial for all Piwi proteins in piRNA amplification and transposon silencing5. Here, we report in vivo evidence that, in contrast to common belief, the catalytic triad of Piwi is not required for the function of PIwi in the germline for stem cell maintenance, fertility, transposon silencing, or piRNA biogenesis. In addition, it is not required for piRNA biogenesis in the soma where Piwi is the sole Piwi-subfamily protein involved in the process. These observations, together with the recent findings on MILI and MIWI2 triad mutant, indicate that even though the slicer function may be required for a subset of piRNA-mediated process, it is overall inconsequential for the function of Piwi proteins Assess the role of the endonuclease activity of Piwi in all known biological processes that involve Piwi function in Drosophila ovary

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Active Promoters give rise to false positive 'Phantom Peaks' in ChIP-Seq experiments

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