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GenomicsCell type-specific chromatin profiling of Drosophila neurons [ChIP-Seq]
Chromatin profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Cell type-specific histone modification maps were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons us...
ORGANISM(S): Drosophila melanogaster 
2012-08-02 | E-GEOD-37032 | biostudies-arrayexpress
GenomicsEpigenome characterization at single base-pair resolution
We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrap...
ORGANISM(S): Saccharomyces cerevisiae 
2011-10-26 | E-GEOD-30551 | biostudies-arrayexpress
GenomicsDynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)
Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped t...
ORGANISM(S): Saccharomyces cerevisiae 
2013-03-01 | E-GEOD-39430 | biostudies-arrayexpress
GenomicsDynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)
Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped t...
ORGANISM(S): Saccharomyces cerevisiae 
2013-03-01 | E-GEOD-39431 | biostudies-arrayexpress
GenomicsHigh-resolution mapping of transcription factor binding sites on native chromatin
Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) and sequencing is widely used for genome-wide profiling of pro...
ORGANISM(S): Drosophila melanogaster 
2013-12-14 | E-GEOD-45672 | biostudies-arrayexpress
TranscriptomicsIdentification of HP1 protein binding sites in Drosophila Kc cells using DamID
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 D...
ORGANISM(S): Drosophila melanogaster 
2007-07-05 | E-MEXP-864 | biostudies-arrayexpress
TranscriptomicsGenome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila
Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem-cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila Kc cells. We found th...
ORGANISM(S): Drosophila melanogaster 
2010-06-11 | E-GEOD-4564 | biostudies-arrayexpress
TranscriptomicsCell type-specific gene expression profiling of Drosophila neurons [RNA-Seq]
Gene expression profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Gene expression profiles were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons in the adult Dro...
ORGANISM(S): Drosophila melanogaster 
2012-08-02 | E-GEOD-37027 | biostudies-arrayexpress
TranscriptomicsIdentification of SUUR protein binding sites in Drosophila Kc cells using DamID
Salivary gland polytene chromosomes of Drosophila melanogaster have a reproducible set of intercalary heterochromatin sites, characterized by late DNA replication, underreplicated DNA, breaks and frequent ectopic contacts. The SuUR mutation has been shown to suppress underreplication, and wild-type ...
ORGANISM(S): Drosophila melanogaster 
2007-07-04 | E-MEXP-863 | biostudies-arrayexpress
GenomicsGenome-wide reductions in active chromatin, paused RNA Polymerase II and nucleosome turnover during heat shock
Heat shock rapidly induces expression of a small set of genes while globally repressing transcription, making it an attractive system for studying alterations in the chromatin landscape that accompany changes in gene regulation. We have characterized these changes using low-salt extraction of intact...
ORGANISM(S): Drosophila melanogaster 
2011-11-15 | E-GEOD-30755 | biostudies-arrayexpress
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