Filter Results
463 results
Here we improved BiTS-ChIP (Bonn et al, Nature Protocols 7, 978-994 (2012)) to identify active enhancer and promoter elements genome wide in the 104 cardiomyocytes that constitute the Drosophila heart tube and represents only ~0.5% of the total cell content of the embryo. A transgenic Drosophila strain expressing nuclear GFP under the control of a cardiac specific enhancer (TinC*>GFP) was used for staged embryo collections at stages 13-14 (10-13h of development). After embryo fixation and dissociation, intact fixed nuclei were fluorescent labelling. Purification of this rare nuclear population was achieved by a two-step sorting procedure, yielding ~98% purity. Chromatin was extracted and used for immunoprecipitation and sequencing (ChIP-seq) to analyze chromatin modifications at promoters (H3K4me3 and H3K27ac) and enhancers (H3K27ac). Two independent biological replicates (from FACS sorting, chromatin preparations and ChIP-Seq) were performed for each mark and sequenced using Illumina HiSeq.
Data Types:
  • Text
We applied ChIP-seq to map the chromosomal binding sites for two nucleosome remodeling complexes containing the ATPase ISWI, ACF and RSF, in Drosophila embryos. Employing a panel of polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters. For further validation we repeated the mapping using chromatin of mutant embryos that do not express ACF1 or RSF1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and give rise to ‘Phantom Peaks’. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin. Examination of various ACF1 and RSF1 antibodies in Drosophila melanogaster embryos which are wildtype or mutant for the antibody targets.
Data Types:
  • Text
[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species ChIP-Seq based binding measurements of six transcription factors in embryos of two Drosophila species, D.melanogaster and D.yakuba.
Data Types:
  • Text
Here we compare the distribution of insulator proteins during interphase and mitosis. We performed ChIP-seq analysis on purified populations of interphase and mitotic Kc cells, using antibodies against CP190, dCTCF, BEAF, and Su(Hw). Examination of 4 different insulator proteins during interphase and mitosis
Data Types:
  • Text
Here we improved BiTS-ChIP (Bonn et al, Nature Protocols 7, 978-994 (2012)) to identify active enhancer and promoter elements genome wide in the 104 cardiomyocytes that constitute the Drosophila heart tube and represents only ~0.5% of the total cell content of the embryo. A transgenic Drosophila strain expressing nuclear GFP under the control of a cardiac specific enhancer (TinC*>GFP) was used for staged embryo collections at stages 13-14 (10-13h of development). After embryo fixation and dissociation, intact fixed nuclei were fluorescent labelling.  Purification of this rare nuclear population was achieved by a two-step sorting procedure, yielding ~98% purity. Chromatin was extracted and used for immunoprecipitation and sequencing (ChIP-seq) to analyze chromatin modifications at promoters (H3K4me3 and H3K27ac) and enhancers (H3K27ac).  Two independent biological replicates (from FACS sorting, chromatin preparations and ChIP-Seq) were performed for each mark and sequenced using Illumina HiSeq.
Data Types:
  • Text
ChIP-seq for the strongest cell cycle regulator transcription factors in Drosophila Melanogaster S2 cells. These assays have been used to validate the direct transcriptional targets of the same transcription factors investigated in RNA-seq (E-MTAB-1364) and Affymetrix microarray experiments (E-MTAB-453). ChIP-seq assays have been done with tagged fusion proteins (for example, since we dont have functional E2f antibodies against endogenous E2f , we are transfecting v5-tagged-E2f-ORF to S2 cells and then use antibodies against v5 to detect the signal from E2f binding). If the ChIP-seq has been done with tagged fusion proteins (such as v5-tagged-E2f-ORF), the protein expression has been induced with CuSO4 treatment 48h prior to cell crosslinking & lysis. Our fusion protein constructs are driven by metallothionein promoter, which is induced by CuSO4. E-MTAB-1648, E-MTAB-1364 and E-MTAB-453 are all data from: Bonke M, et al. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda) 3, 75-90, PMID: 23316440.
Data Types:
  • Text
LID is a histone demethylase acting on H3K4me3, a mark related to transcription and found near the transcription start sites (TSS) of the genes. We analyzed where LID is localized and the effects of LID downregulation in the distribution of H3K4me3. Analysis of LID-binding sites in wild type, and of H3K4me3-binding sites in wild type and LID RNAi wing imaginal discs.
Data Types:
  • Text
  • File Set
This SuperSeries is composed of the following subset Series: GSE31895: ChIP with anti-orc2 antibody to identify regions of orc binding in third instar salivary glands of WT and SuUR mutant Drosophila GSE31896: RNAPolII ChIP to find differences between third instar salivary glands of WT and SuUR GSE31897: ChIP with anti-H3K27me3 to compare binding in salivary glands of WT and SuUR Drosophila GSE31898: CGH to ascertain levels of gDNA in third instar salivary glands of various mutant Drosophila GSE31899: ChIP-Seq of ORC2 bound to third instar salivary gland DNA in WT and mutant Drosophila, analyzed by Illumina sequencing GSE33017: Expression profile of third instar larval salivary gland tissue Refer to individual Series
Data Types:
  • Text
We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species (GSE60428) and HiC analysis in Drosophila melanogaster. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter HiC experiments in wild type drosophila embryos
Data Types:
  • Text
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 using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Three histone modifications were profiled: H3K4me3, H3K27ac, and H3K27me3. Sequencing was performed with an Illumina HiSeq 2000.
Data Types:
  • Text
  • File Set
6