Expression profiling of dme-miR-310 cluster (miR-310, miR-311, miR-312, miR-313) knockout
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE15851 | GEO | 2010/06/25
SECONDARY ACCESSION(S): PRJNA123055
REPOSITORIES: GEO
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Project description:Expression profiling of the dme-miR-310 cluster knockout line in D.melanogaster. The knockout line was generated in an imprecise P-element excision screen using a stock P{EP}2587 containing a P-element insertion directly upstream of the miR-310 cluster. The precise excision line of P{EP}2587 was used as the control. The expression of miR-310 cluster knockout line (imprecise deletion of P{EP}2587 insertion) were compared with the control (precise deletion of P{EP}2587 insertion) using Drosophila Tiling 1.0 F array. Each stock has three biological repeats. A processed data matrix reporting values (log2 intensity after quantile normalization) for all of the Samples is linked below as a supplementary file.
2010-06-24 | E-GEOD-15851 | biostudies-arrayexpress
Project description:The miRNA 310-311-312-313 cluster from D. melanogaster (referred to as Dm310s) and the homolog from D. pseudoobscura (Dp310s) were used to transform D. melanogaster. The over-expression of UAS-miR310s in two Dm310s transgenic lines (M1-7 and M1-3) and Dp310s transgenic line P4-18 was driven by GAL4 line NP5941 with native miR-310 expression pattern. We used Drosophila Tiling 1.0 F arrays to assess the effects of miR310s over-expression on the whole transcriptome. We compared the transcriptional profiling of Dm310s and Dp310s overexpression in D.melanogaster using double-stranded cDNA followed by bioprime random labeling, and hybridization to Affy Drosophila tiling 1.0 F array. Third-instar progeny larvae from the crosses with maternal NP5941 and paternal UAS-miR-310 cluster transgenic lines were collected and third-instar larvae from the cross with maternal NP5941 and paternal w1118 were used as control. Three biological repeats were used for each stock. A processed data matrix reporting values (log2 intensity after quantile normalization) for all of the Samples is linked below as a supplementary file.
2010-06-24 | E-GEOD-15850 | biostudies-arrayexpress
Project description:The miRNA 310-311-312-313 cluster from D. melanogaster (referred to as Dm310s) and the homolog from D. pseudoobscura (Dp310s) were used to transform D. melanogaster. The over-expression of UAS-miR310s in the Dm310s transgenic line M1-7 and Dp310s transgenic line P4-18 was driven by GAL4 line NP5941 with native miR-310 expression pattern. We used DGRC-1 cDNA arrays to assess the effects of miR310s over-expression on the whole transcriptome.
2010-06-25 | GSE15847 | GEO
Project description:The miRNA 310-311-312-313 cluster from D. melanogaster (referred to as Dm310s) and the homolog from D. pseudoobscura (Dp310s) were used to transform D. melanogaster. The over-expression of UAS-miR310s in two Dm310s transgenic lines (M1-7 and M1-3) and Dp310s transgenic line P4-18 was driven by GAL4 line NP5941 with native miR-310 expression pattern. We used Drosophila Tiling 1.0 F arrays to assess the effects of miR310s over-expression on the whole transcriptome.
2010-06-25 | GSE15850 | GEO
Project description:The miRNA 310-311-312-313 cluster from D. melanogaster (referred to as Dm310s) and the homolog from D. pseudoobscura (Dp310s) were used to transform D. melanogaster. The over-expression of UAS-miR310s in the Dm310s transgenic line M1-7 and Dp310s transgenic line P4-18 was driven by GAL4 line NP5941 with native miR-310 expression pattern. We used DGRC-1 cDNA arrays to assess the effects of miR310s over-expression on the whole transcriptome. Direct two-colour design involving six arrays in three dye-swap pairs, with each pair used for the pairwise comparison of Dm310s, Dp310s and w1118 (control).
2010-06-25 | E-GEOD-15847 | biostudies-arrayexpress
Project description:modENCODE_submission_5623 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: Sexed male Jil mutant(official name : Jil-1 z2 genotype : Jil-1 z2/Jil-1z2 outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Developmental Stage: 3rd Instar Larvae Sexed Male; Genotype: Jil-1 z2/Jil-1z2; Sex: Male; Transgene: deletion; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Sexed male Jil mutant(official name : Jil-1 z2 genotype : Jil-1 z2/Jil-1z2 outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Antibody H3K9me3 (new lot) (target is H3K9me3); Developmental Stage 3rd Instar Larvae Sexed Male
2013-03-06 | E-GEOD-44896 | biostudies-arrayexpress
Project description:modENCODE_submission_5602 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: Sexed male Jil mutant-heterozygous(official name : JIL-1z2 genotype : Jil-1 z2/TM3 Ser-GFP outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Developmental Stage: 3rd Instar Larvae Sexed Male; Genotype: Jil-1 z2/TM3 Ser-GFP; Sex: Male; Transgene: deletion; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Sexed male Jil mutant-heterozygous(official name : JIL-1z2 genotype : Jil-1 z2/TM3 Ser-GFP outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Antibody H3K9me2 antibody2 (target is H3K9me2); Developmental Stage 3rd Instar Larvae Sexed Male
2013-03-13 | E-GEOD-45100 | biostudies-arrayexpress
Project description:modENCODE_submission_5619 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: Sexed Female Jil mutant(official name : Jil-1 z2 genotype : Jil-1 z2/ Jil-1 z2 outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Developmental Stage: 3rd Instar Larvae Sexed Female ; Genotype: Jil-1 z2/ Jil-1 z2; Sex: Female; Transgene: deletion; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Sexed Female Jil mutant(official name : Jil-1 z2 genotype : Jil-1 z2/ Jil-1 z2 outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Antibody H4K16ac(M) (target is H4K16ac); Developmental Stage 3rd Instar Larvae Sexed Female
2013-03-13 | E-GEOD-45106 | biostudies-arrayexpress
Project description:modENCODE_submission_5601 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: Sexed male Jil mutant-heterozygous(official name : JIL-1z2 genotype : Jil-1 z2/TM3 Ser-GFP outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Developmental Stage: 3rd Instar Larvae Sexed Male; Genotype: Jil-1 z2/TM3 Ser-GFP; Sex: Male; Transgene: deletion; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Sexed male Jil mutant-heterozygous(official name : JIL-1z2 genotype : Jil-1 z2/TM3 Ser-GFP outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Antibody H3K9me3 (new lot) (target is H3K9me3); Developmental Stage 3rd Instar Larvae Sexed Male
2013-03-06 | E-GEOD-44886 | biostudies-arrayexpress
Project description:modENCODE_submission_5620 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: Sexed male Jil mutant(official name : Jil-1 z2 genotype : Jil-1 z2/Jil-1z2 outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Developmental Stage: 3rd Instar Larvae Sexed Male; Genotype: Jil-1 z2/Jil-1z2; Sex: Male; Transgene: deletion; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Sexed male Jil mutant(official name : Jil-1 z2 genotype : Jil-1 z2/Jil-1z2 outcross : 1 transgene : deletion tags : Transposon tag : none description : - The JIL-1 allele JIL-1z2 was isolated in a screen for imprecise excisions of the EP transposon (Rørth et al. description : 1998) in w; EP(3)3657/?2?3 Sb heterozygotes Antibody H4K16ac(M) (target is H4K16ac); Developmental Stage 3rd Instar Larvae Sexed Male
2013-03-13 | E-GEOD-45107 | biostudies-arrayexpress