Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE55894 | GEO | 2014/07/29
SECONDARY ACCESSION(S): PRJNA241258
REPOSITORIES: GEO
Similar Datasets
Project description:Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines RIP-seq with multiple antibodies to two proteins in two Drosophila cell lines, at least 2 replicates for each IP and input
2014-07-29 | E-GEOD-55894 | biostudies-arrayexpress
Project description:modENCODE_submission_3718 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; NUMBER OF REPLICATES: 6; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) CG8573_RNAi&oldid=39388
2011-10-12 | E-GEOD-32812 | biostudies-arrayexpress
Project description:modENCODE_submission_3719 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) Fly_LacZ_RNAi&oldid=39667
2011-10-12 | E-GEOD-32813 | biostudies-arrayexpress
Project description:Su(Hw) and Shep RIP-seq in Kc and BG3 cell lines
| PRJNA241258 | ENA
Project description:We examined the effects of loss of su(Hw) on gene expression in both carefully staged 3rd instar larvae (selected at the soft white pre-pupae stage) and wing imaginal discs from these animals. su(Hw) null animals were generated by crossing su(Hw)v mutants with a deficiency (Df(3R)ED5644), homozygous individuals were recognised be the lack of the dominat Tb marker carried on the TM6B marker. Keywords: ChIP-chip
2007-07-31 | GSE7682 | GEO
Project description:There is considerable evidence that insulator elements are likely to play a key role in the organisation of the regulatory architecture of the genome. In Drosophila, one of the best studied insulator elements is the gypsy insulator in the gypsy retrotransposon whose function is dependent on the Su(Hw) Zn-finger DNA binding protein. Although there are several hundred Su(Hw) sites in the genome which are proposed to act as endogenous insulator elements, analysis of the role of the Su(Hw) protein has focussed on the gypsy insulator and few endogenous sites have yet been identified. We have used chromatin immunopurification coupled to genomic microarray analysis to identify Su(Hw) binding sites within a representative region of the Drosophila genome; the 3MB Adh region on chromosome 2L. We have located about 60 Su(Hw) binding sites across this region and this has enabled us to construct a robust new Su(Hw) binding site consensus based on these in vivo sites. In contrast to the gypsy insulator which contains 12 Su(Hw) binding sites within 340bp, the endogenous sites are not present in clusters. We identify two key features of these endogenous Su(Hw) sites. Firstly, in contrast to most analyses of DNA binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Secondly, examination of Su(Hw) binding site occupancy in 0-20hr embryos, 3rd larval instar brains or 3rd larval imaginal discs reveals a constant pattern of Su(Hw) binding indicating that most , if not all Su(Hw) sites are constitutively occupied. These two features support a constant genomic architectural role for the Su(Hw) protein. Keywords: ChIP-chip
2006-06-20 | GSE4691 | GEO
Project description:modENCODE_submission_3717 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) CG32491_RNAi&oldid=39662
2011-10-12 | E-GEOD-32811 | biostudies-arrayexpress
Project description:modENCODE_submission_3714 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) CG6384_RNAi&oldid=39664
2011-10-12 | E-GEOD-32808 | biostudies-arrayexpress
Project description:modENCODE_submission_3716 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) Fly_LacZ_RNAi&oldid=39667
2011-10-12 | E-GEOD-32810 | biostudies-arrayexpress
Project description:modENCODE_submission_3715 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody SU(HW)-HB (target is SU(HW)); dsRNA (RNAi_reagent) CG8591_RNAi&oldid=38908
2011-10-12 | E-GEOD-32809 | biostudies-arrayexpress