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ChIP-seq using a Dp1 antibody in Drosophila S2R+ cells

ABSTRACT: Here we report the identification of genomic regions of DNA bound by Dp1 in Drosophila S2R+ cells. Dp1 is a dimerization partner of several E2F transcription factors and is needed for E2F target promoter binding. We find that Dp1 binds the promoter regions of genes important for oxidative phosphorylation. This result is important since our data demonstrates that expression of several oxidative phosphorylation genes is down-regulated in dDP mutant Drosophila 3rd instar larval eye imaginal discs. These ChIP-seq results suggest that the mechanism by which dDP regulates expression of these genes is direct. In addition, we have confirmed a number of these Dp1 bound gene promoters by conventional Chromatin Immunoprecipitation.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE39393 | GEO | 2013/11/25

SECONDARY ACCESSION(S): PRJNA170768

REPOSITORIES: GEO

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ChIP-seq using a Dp1 antibody in Drosophila S2R+ cells

Project description:Here we report the identification of genomic regions of DNA bound by Dp1 in Drosophila S2R+ cells. Dp1 is a dimerization partner of several E2F transcription factors and is needed for E2F target promoter binding. We find that Dp1 binds the promoter regions of genes important for oxidative phosphorylation. This result is important since our data demonstrates that expression of several oxidative phosphorylation genes is down-regulated in dDP mutant Drosophila 3rd instar larval eye imaginal discs. These ChIP-seq results suggest that the mechanism by which dDP regulates expression of these genes is direct. In addition, we have confirmed a number of these Dp1 bound gene promoters by conventional Chromatin Immunoprecipitation. Examination of Dp1 bound regions of genomic DNA in S2R+ cells.

2013-11-25 | E-GEOD-39393 | biostudies-arrayexpress

Gene expression analysis of Drosophila WT and dDP-/- mutant larvae.

Project description:WT and dDP-/- mutant larvae RNAs were analyzed on Drosophila 12 x 135 Nimbelgen gene expression microarrays. dDP-/- mutants are described in Frolov et al., 2001. Genes Dev. Aug 15;15(16):2146-60. PMID: 11511545 The complete elimination of E2F/DP function in Drosophila results in upregulation of DNA damage responses. The net effect of E2F regulation in larval tissues is that all classes of E2F target genes are reppressed by E2F/DP complexes.

2017-11-08 | GSE104544 | GEO

ChIP-seq analysis of M1BP in Drosophila S2R+ cells

Project description:The genomic distribution of a novel transcription factor called M1BP was determined in Drosophila S2R+ cells

2013-08-13 | GSE49842 | GEO

ChIP-seq analysis of M1BP in Drosophila S2R+ cells

Project description:The genomic distribution of a novel transcription factor called M1BP was determined in Drosophila S2R+ cells Polyclonal antibody raised against M1BP was used to immunoprecipitate M1BP-DNA adducts generated by treating Drosophila cells with formaldehyde, lysing the cells, and shearing DNA by sonication. Immunoprecipitated DNA was sequenced using the AB SOLiD system.

2013-08-13 | E-GEOD-49842 | biostudies-arrayexpress

High-throughput sequencing of Drosophila melanogaster small RNAs from S2R+ cells

Project description:High-throughput sequencing of Drosophila melanogaster small RNAs from S2R+ cells. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Small RNAs were sequenced from D. melanogaster S2R+ cells. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt.

2008-12-04 | E-GEOD-13679 | biostudies-arrayexpress

Expression data of wild type, dDP mutant, and de2f1, deleted in the posterior, Drosophila 3rd instar larval eye imaginal discs

Project description:Apoptosis is an important process to eliminate cells from tissue which have incurred irreparable DNA damage. While dE2F1/dDP complexes respond to such damage by transcriptionally activating apoptotic genes, previous data suggests that activation of the previously characterized apoptotic target genes of dE2F1/dDP alone may not be the only gene regulation important for gamma irradiation-induced apoptosis. Here we report that following irradiation in dDP mutant 3rd instar larval eye imaginal discs, many genes important for oxidative phosphorylation are down-regulated, which are not down-regulated following irradiation in wild type eye discs. Biological triplicates of wild type, dDP mutant and de2f1, deleted in the posterior, eye discs were untreated or irradiated with 40Gy of gamma radiation. Total RNA was extracted by Trizol from untreated eye discs and from irradiated eye discs 4h after irradiation. RNA was column purified. PCR amplified RNAs were hybridized on Affymetrix Drosophila Genome 2.0 Array.

2013-11-25 | E-GEOD-39389 | biostudies-arrayexpress

A comparison of transcriptome between Drosophila S2R+ cell line cultured in M3 media supplemented with fly extract and S2R+ cell line cultured in M3 + BPYE + 10% FCS

Project description:We report the transcriptome analysis of Drosophila S2R+ cells cultured in media lacking vertebrate fetal bovine serum during log-phase of growth. The three media conditions are: (1) M3 BPYE 10% FCS (2) M3 + 10% Fex and (3) M3 + 2.5% Fex.

2020-12-22 | GSE154485 | GEO

Pasteurella multocida strain:DP1

Project description:Pasteurella multocida strain:DP1 Genome sequencing

| PRJNA401216 | ENA

High-throughput sequencing of Drosophila melanogaster small RNAs from S2R+ cells

2008-12-04 | GSE13679 | GEO

Expression analysis of Drosophila S2R+ cells depleted of M1BP by RNAi

Project description:Microarray analysis of gene expression profiles in control and M1BP-depleted Drosophila S2R+ cells. The results of this analyses are reported in Li, J. and D.S. Gilmour (2013) The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes. The EMBO J, in press.

2013-08-13 | GSE46629 | GEO

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