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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Insulator protein binding profiles and gene expression analysis of Drosophila melanogaster Kc and Mbn2 cell lines

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE15660: Gene Expression analysis of Kc and Mbn2 cell lines from Drosophila melanogaster. GSE15661: Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells (Set1) GSE15662: Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells (Set2) GSE15663: Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells (Set3) Refer to individual Series

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Ashley Bushey

PROVIDER: E-GEOD-15664 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions.

Bushey Ashley M AM Ramos Edward E Corces Victor G VG

Genes & development 20090514 11

Insulators are protein-bound DNA elements that are thought to play a role in chromatin organization and the regulation of gene expression by mediating intra- and interchromosomal interactions. Suppressor of Hair-wing [Su(Hw)] and Drosophila CTCF (dCTCF) insulators are found at distinct loci throughout the Drosophila melanogaster genome and function by recruiting an additional protein, Centrosomal Protein 190 (CP190). We performed chromatin immunoprecipitation (ChIP) and microarray analysis (ChIP ...[more]

PMID: 19443682

Similar Datasets

Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells

Project description:ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. Three replicates of Su(Hw), dCTCF, and CP190 ChIP-chip experiments in both Kc and Mbn2 cells as well as two replicates of BEAF ChIP-chip experiments in both Kc and Mbn2 cells were compared.

2010-05-19 | E-GEOD-15661 | biostudies-arrayexpress

Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown

Project description:This SuperSeries is composed of the following subset Series: GSE30686: Gene expression analysis of Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown GSE30740: Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells Refer to individual Series

2011-10-13 | E-GEOD-30741 | biostudies-arrayexpress

Distribution of histone modificiation H3K27me3 in Drosophila Kc cells, comparison with dCTCF knockdown

Project description:Here we map the localization of H3K27me3 in Drosophila Kc cells, as well as in Drosophila Kc cells wherein dCTCF is knock down. examination of genomic occupancy for H3K27me3, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740)

2012-06-18 | E-GEOD-37444 | biostudies-arrayexpress

Gene Expression analysis of Kc and Mbn2 cell lines from Drosophila melanogaster.

Project description:Comparison of gene expression between Kc and Mbn2 cell lines derived from Drosophila melanogaster. Microarray analysis was performed with two biological replicates for each cell line. Each array contains 15,634 Drosophila genes in duplicate with 12, 60 mer probes per gene.

2010-05-19 | E-GEOD-15660 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins DREF in Drosophila Kc167 cells

Project description:Here we map the localization of DREF Drosophila replication related element binding factor in Drosophila Kc cells. Examination of genomic occupancy for DREF, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740 and GSE32584). The GSM number for the input for Total Chip_seq data is GSM762849.

2013-05-01 | E-GEOD-39664 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins Mod(mdg4) and L(3)mbt in Kc cells

Project description:Here we map the localization of Mod(mdg4), including Mod(mdg4)2.2 specific and Mod(mdg4) common to all isoforms, to chromatin insulators, as well as the lethal-3 malignant brain tumor protein in Drosophila Kc cells. examination of genomic occupancy for Mod(mdg4)2.2, Mod(mdg4)BTB (all isoforms), and L(3)mbt, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740)

2012-06-18 | E-GEOD-36393 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells

Project description:Here we examine changes in the distribution of Drosophila insulator proteins during the ecdysone response. We performed ChIP-seq analysis in Kc cells at 0, 3, and 48 hours of ecdysone treatment with antibodies against CP190, Su(Hw), dCTCF, and BEAF-32B. Examination of 4 different insulator proteins at 3 time points of ecdysone treatment.

2011-10-13 | E-GEOD-30740 | biostudies-arrayexpress

Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing [ChIP]

Project description:Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologically associating domains (TADs). Borders between TADs are preferentially formed in regions containing high density of active genes and clusters of architectural protein binding sites. Transcription of most genes is turned off during the heat shock response in Drosophila. Here we show that temperature stress induces relocalization of architectural proteins from TAD borders to inside TADs, and this is accompanied by a dramatic rearrangement in the 3D organization of the nucleus. TAD border strength declines, allowing for an increase in long-distance inter-TAD interactions. Similar but quantitatively weaker effects are observed upon inhibition of transcription or depletion of individual architectural proteins. New heat shock-induced inter-TAD interactions result in increased contacts among enhancers and promoters of silenced genes, which recruit Pc and form Pc bodies at the nucleolus. These results suggest that the TAD organization of metazoan genomes is plastic and can be quickly reconfigured to allow new interactions between distant sequences. Analysis of the distribution of architectural proteins, chromatin proteins and histone modifications in Drosophila Kc167 cells. Cells were grown at 25 C (NT) or heat shocked for 20 min at 36.5 C (HS). Both control and reference samples are included. For some of the samples, replicates are also included.

2015-02-24 | E-GEOD-62904 | biostudies-arrayexpress

Two isoforms of Fs(1)h ChIP-seq

Project description:ChIP-seq was performed using Drosophila Kc167 cells using antibodies against the two isoforms of Fs(1)h, the Brd4 homologue. Differences in binding patterns between the two isoforms are described. We examined the differences in Fs(1)h isoform binding across the genome and describe the short isoform to be correlated with transcription at enhancers and promoters. The long isoform is found predominately at insulator binding sites where multiple insulators are bound.

2012-11-15 | E-GEOD-42086 | biostudies-arrayexpress