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Drosophila melanogaster

ABSTRACT: Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [RNA-seq]

PROVIDER: PRJNA305510 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2983120.fastq.gz	Fastqsanger.gz
	SRR2983121.fastq.gz	Fastqsanger.gz
	SRR2983122.fastq.gz	Fastqsanger.gz
	SRR2983123.fastq.gz	Fastqsanger.gz
	SRR2983124.fastq.gz	Fastqsanger.gz

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Drosophila melanogaster

Project description:Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [DamID-seq]

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Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

Project description:Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

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Project description:Tissue-specific DamID profiling of chromatin proteins in Drosophila melanogaster

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Project description:Profiling of Lola-N genomic binding in Drosophila with DamID

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Drosophila melanogaster

Project description:Profiling of Esg genomic binding in the Drosophila midgut with DamID

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Identification of HP1 protein binding sites in Drosophila Kc cells using DamID

Project description:Heterochromatin protein HP1 is thought to play key role in chromatin structure and gene regulation. We performed a genome-wide mapping of HP1 target genes in the non-polytenic Drosophila Kc cells by using DamID. This approach is based on the ability of a chromatin protein fused to Escherichia coli DNA adenine methyltransferase (Dam) to methylate the native binding site of the chromatin protein. Dam-fusion proteins are expressed at very low levels to avoid mistargeting. Subsequently, methylated DNA fragments are isolated, labeled (using Cy3 or Cy5) and hybridized to a microarray. Methylated DNA fragments from cells transfected with Dam alone served as reference. Genomic binding sites of the protein can then be identified based on the targeted methylation pattern. For detailed background information on DamID, see: van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-8 (2001); van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8 (2000). We performed three independent replicates. We used for this study a cDNA array developed by the GeneCore facility in EMBL (Heidelberg, Germany), covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.

2007-07-05 | E-MEXP-864 | biostudies-arrayexpress

Tissue-specific DamID profiling of chromatin proteins in Drosophila melanogaster

Project description:Analysis of gene expression regulation typically requires identification of genomic sites where regulatory proteins bind. For this purpose, ChIP and DamID methods applied to cell lines or model organisms are now routinely used, even in selected cell types. In this work, we present modifications to experimental DamID protocol, as well as a custom data processing algorithm that allows to confidently identify genomic sites enriched with the proteins of interest. This algorithm is implemented in Perl and is also available as executable files thereby making DamID analysis relatively straightforward. Finally, we demonstrate how this pipeline performs when fed with real experimental data.

2016-08-30 | GSE86205 | GEO

Drosophila melanogaster

Project description:Profiling of Islet, Lim3, Hb9 and Eve genomic binding in Drosophila with DamID

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FlyORF-TaDa allows rapid generation of new lines for in vivo cell-type specific profiling of protein-DNA interactions in Drosophila melanogaster

Project description:Targeted DamID (TaDa) is an increasingly popular method of generating cell-type specific DNA binding profiles in vivo. Although sensitive and versatile, TaDa requires the generation of new transgenic fly lines for every protein that is profiled, which is both time-consuming and costly. Here, we describe the FlyORF-TaDa system for converting an existing FlyORF library of inducible open reading frames (ORFs) to TaDa lines via a genetic cross, with recombinant progeny easily identifiable by eye colour. Profiling the binding of the H3K36me3-associated chromatin protein MRG15 in larval neural stem cells using both FlyORF-TaDa and conventional TaDa demonstrates that new lines generated using this system provide accurate and highly-reproducible DamID binding profiles. Our data further show that MRG15 binds to a subset of active chromatin domains in vivo. Courtesy of the large coverage of the FlyORF library, the FlyORF-TaDa system enables the easy creation of TaDa lines for 74% of all transcription factors and chromatin modifying proteins within the Drosophila genome.

2021-01-31 | GSE159632 | GEO

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