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Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

ABSTRACT: The aim of this study is to identify a set of eye-specific genes across Drosophila species. Species are used as replicates to remove biological noise and identify a core set of conserved eye-developmental genes. We analyze this conserved core using the motif discovery tool i-cisTarget, and identify master regulators of retinal determination, including the Zinc Finger transcription factor Glass. Six samples were analyzed by Illumina Digital Gene Expression (DGE) using the NlaIII restriction enzyme, namely two different tissues (eye-antennal discs and wing discs) for each of the three species under study.

ORGANISM(S): Drosophila virilis

SUBMITTER: Stein Aerts

PROVIDER: E-GEOD-39782 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Tag-seq in eye-antennal and wing imaginal discs of D.melanogaster, D.yakuba, and D.virilis; RNA-seq in wild-type and glass mutant D.melanogaster eye-antennal imaginal discs.

Project description:In this study we use Tag-sequencing in eye-antennal and wing imaginal discs across Drosophila species to determine a set of conserved eye-specific developmental genes. Next, we perform motif discovery analysis using the tool i-cisTarget, to depict the core gene developmental network underlying compound eye photoreceptor. The Glass position weight matrix appears as the most highly overrepresented motif, thus positioning Glass as a master regulator in compound eye photoreceptor development. Differential gene expression analysis by RNA-seq in D.melanogaster wild-type eye-antennal versus glass mutant [gl 60j] shows that the majority of our predicted Glass targets show strong downregulation in the glass mutant. This SuperSeries is composed of the following subset Series: GSE39781: RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster GSE39782: Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

2012-09-21 | E-GEOD-39784 | biostudies-arrayexpress

modENCODE_White Lab: genome-wide ChIP-chip and ChIP-seq data [D. yakuba H3K27me3]

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2013-09-13 | E-GEOD-50819 | biostudies-arrayexpress

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Project description:[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species ChIP-Seq based binding measurements of six transcription factors in embryos of two Drosophila species, D.melanogaster and D.yakuba.

2010-02-18 | E-GEOD-20369 | biostudies-arrayexpress

Genome-wide comparative ChIP-seq data of CTCF and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer

Project description:This is a dataset which comprises the following two different kinds of genomic data in Drosophila species: First, triplicate ChIP-seq data of CTCF (CCCTC binding factor) binding profiles in each of the four closely related Drosophila species : Drosophila melanogaster, Drosophila simulans, Drosophila yakuba and Drosophila pseudoobscura at white pre pupa stage; Second, triplicate RNA-seq data of white pre pupa whole animals of three Drosophila species: Drosophila melanogaster, Drosophila simulans and Drosophila yakub. The binding site/region/peaks are called using a modified method of QuEST( please see details in our related publication). The sequence read counts and RPKM values are calculated following the method in Mortazavi et al 2008 Nature Methods paper. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of CTCF binding in 4 Drosophila species and their correlation with gene expression levels in the same development stages

2012-11-08 | E-GEOD-24449 | biostudies-arrayexpress

A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity

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2010-07-01 | E-GEOD-21503 | biostudies-arrayexpress

Genome-wide comparative ChIP-seq data of H3K27me3 and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer

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2013-08-17 | E-GEOD-49945 | biostudies-arrayexpress

ChIP-Seq of six Drosophila species with anti-Drosophila melanogaster Twist and anti-Snail antibodies using different library fragment sizes

Project description:The binding patterns of some transcription factors have been shown to diverge substantially between closely related species. Here, we show that the binding pattern of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at developmental enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their cooperative binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. We predict that conservation, dynamic occupancy, and combinatorial regulation will be generally true for developmental enhancers.

2010-12-07 | E-MTAB-376 | biostudies-arrayexpress

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

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2013-12-01 | E-GEOD-35842 | biostudies-arrayexpress

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2012-04-13 | E-GEOD-31235 | biostudies-arrayexpress

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity [RNA-Seq]

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2012-04-13 | E-GEOD-31234 | biostudies-arrayexpress

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