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Time course Pho/dSfmbt Chromatin Immunoprecipitation on Drosophila melanogaster embryos during embryogenesis

ABSTRACT: Time course Pho/dSfmbt Chromatin Immunoprecipitation on Drosophila melanogaster embryos during embryogenesis

PROVIDER: PRJEB13498 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1358770.fastq.gz	Fastqsanger.gz
	ERR1358771.fastq.gz	Fastqsanger.gz
	ERR1358772.fastq.gz	Fastqsanger.gz
	ERR1358773.fastq.gz	Fastqsanger.gz
	ERR1358774.fastq.gz	Fastqsanger.gz

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Time course Pho/dSfmbt Chromatin Immunoprecipitation on Drosophila melanogaster embryos during embryogenesis

Project description:Here we improved BiTS-ChIP (Bonn et al, Nature Protocols 7, 978-994 (2012)) to identify active enhancer and promoter elements genome wide in the 104 cardiomyocytes that constitute the Drosophila heart tube and represents only ~0.5% of the total cell content of the embryo. A transgenic Drosophila strain expressing nuclear GFP under the control of a cardiac specific enhancer (TinC*>GFP) was used for staged embryo collections at stages 13-14 (10-13h of development). After embryo fixation and dissociation, intact fixed nuclei were fluorescent labelling.Â Â Purification of this rare nuclear population was achieved by a two-step sorting procedure, yielding ~98% purity. Chromatin was extracted and used for immunoprecipitation and sequencing (ChIP-seq) to analyze chromatin modifications at promoters (H3K4me3 and H3K27ac) and enhancers (H3K27ac).Â Â Two independent biological replicates (from FACS sorting, chromatin preparations and ChIP-Seq) were performed for each mark and sequenced using Illumina HiSeq.

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Project description:ChIP followed by next generation sequencing over 5 developmental time points of Drosophila virilis embryos (w[-], white eye mutation line) against 5 key mesodermal factors (Twist, Tinman, Mef2, Bagpipe and Biniou) were performed. The aim was to compare binding profiles of these 5 mesodermal factors between two Drosophila species, D. melanogaster (Zinzen et al., 2009) and D. virilis (this study). D. virilis specific antibodies were used for this purpose for 4 of the 5 factors (D. melanogaster Anti-body for Mef2 showed high specificity in D. virilis). Two biological replicates for each condition were sequenced using Illumina HiSeq.

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Project description:Drosophila melanogaster is a well-studied genetic model organism with several large-scale transcriptome resources. Here we investigate 7,952 proteins during the fly life cycle from embryo to adult and also provide a high-resolution temporal time course proteome of 5,458 proteins during embryogenesis. We use our large scale data set to compare transcript/protein expression, uncovering examples of extreme differences between mRNA and protein abundance. In the embryogenesis proteome, the time delay in protein synthesis after transcript expression was determined. For some proteins, including the transcription factor lola, we monitor isoform specific expression levels during early fly development. Furthermore, we obtained firm evidence of 268 small proteins, which are hard to predict by bioinformatics. We observe peptides originating from non-coding regions of the genome and identified Cyp9f3psi as a protein-coding gene. As a powerful resource to the community, we additionally created an interactive web interface (http://www.butterlab.org) advancing the access to our data.

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