Small RNA sequencing of control and Su(var)3-7 mutant Drosophila ovary
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Denis Basquin
PROVIDER: E-GEOD-53015 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:mRNA expression levels were determined by NGS for wildtype larvae as well as for larvae lacking HP1a [Su(var)205^04/Su(var)205^05 transheterozygotes].
2012-09-01 | GSE39083 | GEO
Project description:Histone modifications are a class of epigenetic marks with prominent roles in gene regulation in eukaryotes. One such mark, predominantly inactivation-related, is methylation of histone H3 lysine 9 (H3K9). In the present study, we decipher the interplay between two evolutionary conserved Drosophila H3K9-specific histone methyltransferases, SU(VAR)3-9 and SETDB1. We asked whether SETDB1 is required for targeting of SU(VAR)3-9. Using DamID-seq, we obtained SU(VAR)3-9 binding profiles for the chromosomes from larval salivary glands and germline cells from adult females, and compared profiles between the wild type and SETDB1-mutant backgrounds. Our analyses indicate that the vast majority of single-copy genes in euchromatin are targeted by SU(VAR)3-9 only in the presence of SETDB1, whereas repeated sequences in heterochromatin is largely SETDB1-independent. Interestingly, piRNA clusters 42AB and 38C behave differently in terms of SU(VAR)3-9 binding in somatic and germline cells. Namely, SU(VAR)3-9 binding to these piRNA clusters is independent of SETDB1 in somatic cells, whereas it is SETDB1-dependent in the germline. In addition, we compared SU(VAR)3-9 profiles in female germline cells at different developmental stages (whole juvenile ovaries and mature nurse cells). It turned out that SU(VAR)3-9 binding is influenced both by the presence of SETDB1, as well as by the differentiation stage.
2019-07-16 | GSE134250 | GEO
Project description:modENCODE_submission_4943 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages 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-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type; EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody Su(var)3-7-Q3448 (target is Su(var)3-7); Developmental Stage Embryo 14-16hr OR
2013-05-28 | E-GEOD-47250 | biostudies-arrayexpress
Project description:modENCODE_submission_5127 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages 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-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type; EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody Su(var)3-7-Q3448 (target is Su(var)3-7); Developmental Stage 3rd Instar Larvae
2013-05-28 | E-GEOD-47307 | biostudies-arrayexpress
Project description:modENCODE_submission_5606 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages 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-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type; EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody Su(var)3-7-Q3448 (target is Su(var)3-7); Developmental Stage Mixed Adult
2013-05-28 | E-GEOD-47334 | biostudies-arrayexpress
Project description:modENCODE_submission_3889 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. 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: Strain: Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9^06/Su(var)3-9^17; Transgene: n/a; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44502 | biostudies-arrayexpress
Project description:modENCODE_submission_3892 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages 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: Strain: Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9^06/Su(var)3-9^17; Transgene: n/a; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Antibody HP1 wa191 (target is HP1a); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44504 | biostudies-arrayexpress
Project description:modENCODE_submission_3888 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. 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: Strain: Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9^06/Su(var)3-9^17; Transgene: n/a; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Antibody H3K36me3 abcam (target is H3K36me3); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44501 | biostudies-arrayexpress
Project description:modENCODE_submission_3891 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. 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: Strain: Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9^06/Su(var)3-9^17; Transgene: n/a; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Antibody H3K9me3 abcam (target is H3K9me3); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44503 | biostudies-arrayexpress
Project description:modENCODE_submission_4124 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. 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: Strain: Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9^06/Su(var)3-9^17; Transgene: n/a; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Antibody H3K9me1 (new lot 2) (target is H3K9me1); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44514 | biostudies-arrayexpress