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CUTnTag against Beaf-32, CP190 and CTCF in Drosophila melanogaster wild-type and insulator-depleted embryos at stage NC14

ABSTRACT: CUTnTag against Beaf-32, CP190 and CTCF in Drosophila melanogaster wild-type and insulator-depleted embryos at stage NC14

PROVIDER: PRJEB54783 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9966550_1.fastq.gz	Fastqsanger.gz
	ERR9966550_2.fastq.gz	Fastqsanger.gz
	ERR9966551_1.fastq.gz	Fastqsanger.gz
	ERR9966551_2.fastq.gz	Fastqsanger.gz
	ERR9966552_1.fastq.gz	Fastqsanger.gz

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CUTnTag against Beaf-32, CP190 and CTCF in Drosophila melanogaster wild-type and insulator-depleted embryos at stage NC14

Project description:CUTnTag against Beaf-32, CP190 and CTCF was performed in wild-type and insulator-depleted embryos collected between 2h10 and 2h40 after egg laying (corresponding to the stage NC14). Spike-ins from D. virilis were used in each reaction. For each sample, 50k nuclei from each species were mixed together at the start of the protocol. For each protein, CUTnTag was done in biological duplicates. Sequencing was performed on Illumina NextSeq 500.

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Poly(A) mRNA-seq of Drosophila embryos at NC14 depleted of Beaf-32, CTCF or CP190

Project description:Profiling of genes expression changes caused by the depletion of either Beaf-32, CP190 or CTCF during early embryogenesis. Gene expression changes were profiled in embryos at NC14 (manually-selected). Beaf-32 and CP190 were depleted using RNAi and CTCF by using maternal/zygotic null embryos. Poly(A) mRNA-seq was performed from three biological replicates.

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Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify binding sites of Beaf-32, CP190, CTCF, Su(Hw) and GAF insulator proteins

Project description:ChIP-seq against Beaf-32, CP190, CTCF, Su(Hw) and GAF was performed in wild-type embryos collected between 2h10 and 2h40 after egg laying (corresponding to the stage NC14). For each protein, ChIP-seq was done in biological duplicates. Matched input controls were also generated. Sequencing was performed on Illumina NextSeq 500.

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Hi-C in Drosophila embryos at NC14 depleted of Beaf-32, CP190 or CTCF using the Bridge Adaptor Protocol

Project description:Hi-C was performed using the Bridge Adaptor Protocol in 2 biological replicates of Drosophila embryos at NC14 depleted of the maternal deposition of Beaf-32, CP190 or CTCF mRNA and protein. Embryos were collected at 2-3h AEL and were derived from mothers expressing RNAi against Beaf-32 or CP190 in the germline, or were genetic null for the maternal and zygotic contribution of CTCF.

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Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. Binding profiles of CP190 in stably transfected Drosophila S2 cell lines expressing in Wild-Type Beaf (Control) or Mutant Beaf by ChIP-Seq (Illumina)

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2014-02-01 | E-GEOD-52962 | biostudies-arrayexpress

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