title: HP1b Q4113.Kc

summary:
modENCODE_submission_4127
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line Kc167; Antibody HP1b Q4113 (target is HP1b)

last: Elgin


title: H3K9me1 (new lot 2).D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 06_17 Mutant

status: Public on Feb 22 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

type: Genome binding/occupancy profiling by genome tiling array

summary:
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

overall_design: 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

first: Gary

last: Karpen

first: Sarah

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: MRG15_Q2482.S2

summary:
modENCODE_submission_3950
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

overall_design: 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 MRG15 Q2482 (target is MRG15)


title: LSD1_Q3430.S2

summary:
modENCODE_submission_3949
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

overall_design: 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 LSD1 Q3430 (target is LSD1)


title: HP4 Q4072.S2

summary:
modENCODE_submission_3948
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

overall_design: 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: 5;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody HP4 Q4072 (target is HP4)


title: dmTopo II(DAJ).S2

summary:
modENCODE_submission_3945
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

overall_design: 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 dmTopo II(DAJ) (target is dmTopo II)


title: HP2 (Ab2-90).2-4 hr OR embryo

summary:
modENCODE_submission_3944
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 2-4hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody HP2 (Ab2-90) (target is HP2); Developmental Stage Embryo 2-4hr OR


title: PIWI-Q2569.D.mel 3rd Instar Larvae Nuclei piwi2 mutant

summary:
modENCODE_submission_3951
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: PIWI2 mutant; Developmental Stage: 3rd Instar Larvae; Genotype: piwi2/piwi2; Transgene: P{ry11};  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain PIWI2 mutant; Antibody PIWI-Q2569 (target is PIWI); Developmental Stage 3rd Instar Larvae


title: POF (MO 459).D.mel 3rd Instar Larvae Nuclei HP1a Mutant

summary:
modENCODE_submission_3896
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1a mutant
Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)205 [4]/Su(var)205 [5]; Transgene: none;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain HP1a mutant
Antibody POF (MO 459) (target is POF); Developmental Stage 3rd Instar Larvae


title: HP1 wa191.D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 06_17 Mutant

summary:
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

overall_design: 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


title: POF (MO 459).14-16 hr OR embryo

summary:
modENCODE_submission_3895
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody POF (MO 459) (target is POF); Developmental Stage Embryo 14-16hr OR


title: H3K9me3 abcam.D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 06_17 Mutant

summary:
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

overall_design: 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


title: H3K27me1.S2

summary:
modENCODE_submission_3943
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

overall_design: 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: 6;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K27me1 (target is H3K27me1)


title: RNA Pol II (abcam).D.mel 3rd Instar Larvae Nuclei HP1a Mutant

summary:
modENCODE_submission_3798
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1a mutant
Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)205 [4]/Su(var)205 [5]; Transgene: none;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain HP1a mutant
Antibody RNA Pol II (abcam) (target is PolII); Developmental Stage 3rd Instar Larvae


title: Su(var)3-9-Q2598.OR Head Nuclei

summary:
modENCODE_submission_3802
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody Su(var)3-9-Q2598 (target is Su(var)3-9); Developmental Stage Mixed Adult


title: H3K18Ac_14-16h_embryos_mixedABlot

summary:
modENCODE_submission_3886
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K18ac (target is H3K18ac); Developmental Stage Embryo 14-16hr OR


title: POF (MO 459).D.mel 3rd Instar Larvae Nuclei POF Mutant

summary:
modENCODE_submission_3794
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: POF mutant
Developmental Stage: 3rd Instar Larvae; Genotype: POF [D119]/POF [D119]; Transgene: deletion;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain POF mutant
Antibody POF (MO 459) (target is POF); Developmental Stage 3rd Instar Larvae


title: H3K36me3 abcam.D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 06_17 Mutant

summary:
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

overall_design: 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


title: POF (MO 459).OR Head Nuclei

summary:
modENCODE_submission_3796
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody POF (MO 459) (target is POF); Developmental Stage Mixed Adult


title: POF (MO 459).D.mel 3rd Instar Larvae Nuclei EGG Mutant

summary:
modENCODE_submission_3793
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: EGG mutant
Developmental Stage: 3rd Instar Larvae; Genotype: EGG [10.1-1a]/EGG [10.1-1a];  NUMBER OF REPLICATES: 5;  EXPERIMENTAL FACTORS: Strain EGG mutant
Antibody POF (MO 459) (target is POF); Developmental Stage 3rd Instar Larvae


title: HP1 wa191.D.mel 3rd Instar Larvae Nuclei POF Mutant

summary:
modENCODE_submission_3780
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: POF mutant
Developmental Stage: 3rd Instar Larvae; Genotype: POF [D119]/POF [D119]; Transgene: deletion;  NUMBER OF REPLICATES: 5;  EXPERIMENTAL FACTORS: Strain POF mutant
Antibody HP1 wa191 (target is HP1a); Developmental Stage 3rd Instar Larvae


title: HP1b Q4114.OR Head Nuclei

summary:
modENCODE_submission_3778
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody HP1b Q4114 (target is HP1b); Developmental Stage Mixed Adult


title: HP2 (Ab2-90).OR Head Nuclei

summary:
modENCODE_submission_3781
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody HP2 (Ab2-90) (target is HP2); Developmental Stage Mixed Adult


title: H3K9me2-Ab2 (new lot).OR Head Nuclei

summary:
modENCODE_submission_3773
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage Mixed Adult


title: H3K9me3 abcam.D.mel 3rd Instar Larvae Nuclei EGG Mutant

summary:
modENCODE_submission_3774
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: EGG mutant
Developmental Stage: 3rd Instar Larvae; Genotype: EGG [10.1-1a]/EGG [10.1-1a];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain EGG mutant
Antibody H3K9me3 abcam (target is H3K9me3); Developmental Stage 3rd Instar Larvae


title: H3K9me2-Ab2 (new lot).D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 06_17 Mutant

summary:
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

overall_design: 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


title: HP1c (MO 462).OR Head Nuclei

summary:
modENCODE_submission_3779
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody HP1c (MO 462) (target is HP1c); Developmental Stage Mixed Adult


title: H3K9ac.OR Head Nuclei

summary:
modENCODE_submission_3766
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody H3K9ac (target is H3K9ac); Developmental Stage Mixed Adult


title: H3K9me3 abcam.D.mel 3rd Instar Larvae Nuclei HP1a Mutant

summary:
modENCODE_submission_3775
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1a mutant
Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)205 [4]/Su(var)205 [5]; Transgene: none;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain HP1a mutant
Antibody H3K9me3 abcam (target is H3K9me3); Developmental Stage 3rd Instar Larvae


title: H3K9ac.14-16 hr OR embryo

summary:
modENCODE_submission_3764
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K9ac (target is H3K9ac); Developmental Stage Embryo 14-16hr OR


title: H3K23ac.OR Head Nuclei

summary:
modENCODE_submission_3756
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody H3K23ac (target is H3K23ac); Developmental Stage Mixed Adult


title: H3K36me3 abcam.D.mel 3rd Instar Larvae Nuclei HP1a Mutant

summary:
modENCODE_submission_3759
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1a mutant
Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)205 [4]/Su(var)205 [5]; Transgene: none;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain HP1a mutant
Antibody H3K36me3 abcam (target is H3K36me3); Developmental Stage 3rd Instar Larvae


title: H3K9acS10P (new lot).OR Head Nuclei

summary:
modENCODE_submission_3767
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Mixed Adult; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); tissue (organism part) ; Antibody H3K9acS10P (new lot) (target is H3K9acS10P); Developmental Stage Mixed Adult


title: H3K9me2-Ab2 (new lot).D.mel 3rd Instar Larvae Nuclei HP1a Mutant

summary:
modENCODE_submission_3771
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1a mutant
Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)205 [4]/Su(var)205 [5]; Transgene: none;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain HP1a mutant
Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae


title: Chro(Chriz)WR.14-16 hr OR embryo

summary:
modENCODE_submission_3746
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody Chro(Chriz)WR (target is Chriz); Developmental Stage Embryo 14-16hr OR


title: H3K18Ac (new lot).14-16 hr OR embryo

summary:
modENCODE_submission_3754
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 6;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H3K18Ac (new lot) (target is H3K18Ac); Developmental Stage Embryo 14-16hr OR


title: RNA Pol II (abcam).D.mel 3rd Instar Larvae Nuclei HP1c Mutant

summary:
modENCODE_submission_3711
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1c mutant(official name : HP1c[f04929] genotype : w[1118]; PBac{w[+mC]=WH}HP1c[f04929] outcross : unknown transgene : PBac insertion tags : Transposon description : Insertion of PBac transgene disrupts Hp1c gene (Gene disruption project).


title: HP1 wa191.D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 Mutant

summary:
modENCODE_submission_3706
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Su(var)3-9 mutant

Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9 [6]/Su(var)3-9 [6];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Su(var)3-9 mutant
Antibody HP1 wa191 (target is HP1a); Developmental Stage 3rd Instar Larvae


title: HP1 wa191.D.mel 3rd Instar Larvae Nuclei EGG Mutant

summary:
modENCODE_submission_3702
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: EGG mutant
Developmental Stage: 3rd Instar Larvae; Genotype: EGG [10.1-1a]/EGG [10.1-1a];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain EGG mutant
Antibody HP1 wa191 (target is HP1a); Developmental Stage 3rd Instar Larvae


title: HP1 wa191.D.mel 3rd Instar Larvae Nuclei mt2 Mutant

summary:
modENCODE_submission_3703
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: mt2 mutant(official name : MT2 [149] mutant genotype : Mt2 [149]/Mt2 [149] outcross : unknown tags : Transposon description : Mobilization of the progenitor insertion P{EP}GE15695. 59bp of 5' P{EP} sequence are present at the transcriptional start site description : along with a 4bp duplication of coding sequences. The mutation results in a frameshift.
Developmental Stage: 3rd Instar Larvae; Genotype: Mt2 [149]/Mt2 [149];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain mt2 mutant(official name : MT2 [149] mutant genotype : Mt2 [149]/Mt2 [149] outcross : unknown tags : Transposon description : Mobilization of the progenitor insertion P{EP}GE15695. 59bp of 5' P{EP} sequence are present at the transcriptional start site description : along with a 4bp duplication of coding sequences. The mutation results in a frameshift.
Antibody HP1 wa191 (target is HP1a); Developmental Stage 3rd Instar Larvae


title: H4K16ac(M).14-16 hr OR embryo

summary:
modENCODE_submission_3698
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H4K16ac(M) (target is H4K16ac); Developmental Stage Embryo 14-16hr OR


title: H3K9me1 (Diagenode).S2

summary:
modENCODE_submission_4182
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

overall_design: 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: 8;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3K9me1 (Diagenode) (target is H3K9me1)


title: H3K9me3 abcam.D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 Mutant

summary:
modENCODE_submission_3696
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Su(var)3-9 mutant

Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9 [6]/Su(var)3-9 [6];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Su(var)3-9 mutant
Antibody H3K9me3 abcam (target is H3K9me3); Developmental Stage 3rd Instar Larvae


title: H3K36me3 abcam.D.mel 3rd Instar Larvae Nuclei EGG Mutant

summary:
modENCODE_submission_3684
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: EGG mutant
Developmental Stage: 3rd Instar Larvae; Genotype: EGG [10.1-1a]/EGG [10.1-1a];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain EGG mutant
Antibody H3K36me3 abcam (target is H3K36me3); Developmental Stage 3rd Instar Larvae


title: H3K36me3 abcam.D.mel 3rd Instar Larvae Nuclei POF Mutant

summary:
modENCODE_submission_3686
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: POF mutant
Developmental Stage: 3rd Instar Larvae; Genotype: POF [D119]/POF [D119]; Transgene: deletion;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain POF mutant
Antibody H3K36me3 abcam (target is H3K36me3); Developmental Stage 3rd Instar Larvae


title: HP1b (Henikoff).D.mel 3rd Instar Larvae Nuclei

summary:
modENCODE_submission_3018
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody HP1b (Henikoff) (target is HP1b); Developmental Stage 3rd Instar Larvae


title: H4K16ac(L).14-16 hr OR embryo

summary:
modENCODE_submission_3697
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 14-16hr OR; Genotype: wild type;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Antibody H4K16ac(L) (target is H4K16ac); Developmental Stage Embryo 14-16hr OR


title: Su(var)3-7-Q3448.D.mel 3rd Instar Larvae Nuclei

summary:
modENCODE_submission_3059
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

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: 3rd Instar Larvae; Genotype: wild type;  NUMBER OF REPLICATES: 4;  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


title: HP1b (Henikoff).BG3

summary:
modENCODE_submission_3016
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

overall_design: 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 HP1b (Henikoff) (target is HP1b)


title: HP1c (MO 462).D.mel 3rd Instar Larvae Nuclei HP1a Mutant

summary:
modENCODE_submission_3701
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1a mutant
Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)205 [4]/Su(var)205 [5]; Transgene: none;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain HP1a mutant
Antibody HP1c (MO 462) (target is HP1c); Developmental Stage 3rd Instar Larvae


title: Genome-wide binding of Sd and Yki in imaginal discs

status: Public on Oct 03 2012

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

country: USA

institute: University of Minnesota Medical School

summary:
The transcription cofactor Yki drives growth and proliferation in part by controlling mitochondrial network formation. To determine if Yki and Sd are directly bound to DNA corresponding to mitochondrial genes, we used chromatin immunoprecipitation and whole genome tiling arrays (ChIP-chip) to identify regions bound by these factors in eye-antenna and wing imaginal discs.

The supplementary .bed files contain all Yki or Sd binding sites (called at 5% FDR) in wing or eye-antenna imaginal discs, as well as shared Sd+Yki sites and associated target genes.

overall_design: Wing or eye-antenna imaginal discs ChIPped for Yki or Sd-GFP vs. input DNA from corresponding imaginal discs.

first: Nicolas

last: Negre

first: Kevin

middle: P

last: White

first: Richard

middle: S

last: Mann

first: Raghavendra

last: Nagaraj

first: Shubha

last: Rao

last: Jones

first: Heather

last: Christofk

first: Utpal

last: Banerjee


title: Gametogenesis in an alternative hermaphrodite mollusk, the Pacific Oyster Crassostrea gigas: a microarray-based analysis identifies stage- and sex-specific genes

status: Public on Dec 01 2012

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

country: France

institute: Universite de caen

summary:
Background
The Pacific oyster Crassostrea gigas (Mollusca, Lophotrochozoa) is an alternative and irregular protandrous hermaphrodite. Little is known about the genetic and phenotypic bases of sex determinism in oysters, and little more about the molecular pathways regulating reproduction. We have recently developed and validated a microarray containing 31,918 oligomers (Dheilly et al., 2011) representing the oyster transcriptome. The application of this microarray to the study of mollusks gametogenesis should provide a better understanding of the key factors involved in sex differentiation and the regulation of oyster reproduction.

Results
Expression of the 31,918 ESTs was studied in gonads of oysters cultured along the French Atlantic coasts over a yearly reproductive cycle. Principal component analysis and hierarchical clustering first showed a significant divergence in gene expression patterns of males and females beginning when gonial mitosis started. Early expressed male-specific genes included bindin and female-specific genes included foxL2, a pancreatic lipase related protein, cd63 and vitellogenin. ANOVA analysis of the data further revealed 2482 genes differentially expressed during the course of males and/or females gametogenesis. The expression of 434 genes could be localized in either germ cells or somatic cells of the gonad by comparing the transcriptome of gonads to the transcriptomes of striped oocytes and somatic tissues. Analysis of the annotated genes revealed conserved molecular mechanisms between mollusks and mammals. Genes involved in chromatin condensation, DNA replication and repair, mitosis and meiosis regulation, transcription, translation and apoptosis were expressed in both male and female gonads. Additional lists of genes more specifically involved in either spermatogenesis (meiotic phase, in spermatozoids and mature sperm formation and in flagella structure and movement) or oogenesis (female sex differentiation, transcriptional regulation, cell cycle regulation and oocytes maturation) were also generated.

Conclusions
Our study provides novel insight into spermatogenesis and oogenesis in an alternative hermaphrodite bivalve, the Pacific oyster C. gigas. We identified genes opening new perspectives for functional studies of the signaling pathways implicated in gonad differentiation and development.

overall_design: Individual gonad oysters were sampled in 3 sites: site 1 = Locmariaquer (Brittany, France), site 2 = Baie des Veys (Normandy, France), and site 3 = Argenton (Brittany, France). 8 undifferentiated stage 0 gonads from site 1 were processed. 4 individuals from site 1 were processed for each gonad developmental stage and sex: stage 1 male, stage 1 female, stage 2 male, stage 2 female, stage 3 male, and stage 3 female. Pools of stage 3 females were prepared with individuals from site 1 and site 2 for biological validation of the results. Striped gonads from stage 3 females were prepared for prediction of gene expression localization.

middle: M

first: Christophe

last: Lelong

first: Arnaud

last: Huvet

first: Pierre

last: Boudry

first: Pascal

last: Favrel

first: Guillaume

last: Riviere

first: Kristell

last: Kellner

first: Marie

last: Dubos


title: H3K9me2-Ab2 (new lot).D.mel 3rd Instar Larvae Nuclei mt2 Mutant

first: DCC

last: modENCODE

summary:
modENCODE_submission_3693
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: mt2 mutant(official name : MT2 [149] mutant genotype : Mt2 [149]/Mt2 [149] outcross : unknown tags : Transposon description : Mobilization of the progenitor insertion P{EP}GE15695. 59bp of 5' P{EP} sequence are present at the transcriptional start site description : along with a 4bp duplication of coding sequences. The mutation results in a frameshift.
Developmental Stage: 3rd Instar Larvae; Genotype: Mt2 [149]/Mt2 [149];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain mt2 mutant(official name : MT2 [149] mutant genotype : Mt2 [149]/Mt2 [149] outcross : unknown tags : Transposon description : Mobilization of the progenitor insertion P{EP}GE15695. 59bp of 5' P{EP} sequence are present at the transcriptional start site description : along with a 4bp duplication of coding sequences. The mutation results in a frameshift.
Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: H3K9me2-Ab2 (new lot).D.mel 3rd Instar Larvae Nuclei EGG Mutant

summary:
modENCODE_submission_3692
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: EGG mutant
Developmental Stage: 3rd Instar Larvae; Genotype: EGG [10.1-1a]/EGG [10.1-1a];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain EGG mutant
Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae


title: H3K4me2_JBC 1360331.D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 Mutant

summary:
modENCODE_submission_3690
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Su(var)3-9 mutant
Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9 [6]/Su(var)3-9 [6];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Su(var)3-9 mutant
Antibody H3K4me2 JBC 1360331 (target is H3K4me2); Developmental Stage 3rd Instar Larvae


title: H3K9me2-Ab2 (new lot).D.mel 3rd Instar Larvae Nuclei Su(var) 3-9 Mutant

summary:
modENCODE_submission_3695
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

overall_design:
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Su(var)3-9 mutant

Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9 [6]/Su(var)3-9 [6];  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Strain Su(var)3-9 mutant
Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae


title: miRNA microarray of mice with unilateral ureteral obstruction

status: Public on Dec 05 2012

city: Tokyo

first: Ryuji

last: Morizane

address: 35 shinanomachi, shinjukuku

department: Internal Medicine

country: Japan

institute: Keio University School of Medicine

summary:
To find miRNAs that involve in renal epithelial transition and renal fibrosis, we performed unilateral ureteral obstruction of mice for 7 days. After that, we harvested kidneys, and performed microarray of miRNA. Contralateral kidneys without ureteral obstruction were used as controls.
miRNAs were purified from kidneys with ureteral obstruction and contralateral kidneys without ureteral obstruction. Then microarray of miRNA was performed (n=4). miRNAs up-regulated in kidneys with ureteral obsctruction compared with contralateral kidneys were sorted.

overall_design: We performed unilateral ureteral obstruction of mice for 7 days, and harvested kidneys.

first: Toshiaki

last: Monkawa


title: Histone chaperone NAP1 is required for sister chromatid resolution

status: Public on Jul 26 2012

city: Rotterdam

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

summary: The fidelity of chromosome duplication through cell divisions requires timely binding and release of the cohesin. Cohesin is a ring-shaped protein complex linking newly replicated sister chromatids to ensure their appropriate transmission through mitosis. Upon commencement of mitosis cohesin is removed from DNA in two steps: first, from chromosome arms resulting in sister chromatid resolution, and, second, from centromers leading to sister chromatid segregation. As DNA of eukaryotic chromosomes is assembled into chromatin, regulation of sister chromatid cohesion-segregation may involve chromatin modifying machinery, but this link is not well understood. Here we report that H2A-H2B histone chaperone NAP1, a factor, which is primarily implicated in chromatin assembly, is required for cohesin release from mitotic chromosome arms. NAP1 and cohesin protein complex interact directly and share multiple binding sites on chromatin. Depletion of the NAP1 hinders cohesin removal during mitosis resulting in accumulation of unresolved sister chromatids. Thus, in addition to its well established functions in chromatin dynamics, histone chaperone NAP1 coordinates cell cycle dependent cohesin release. These results reveal a novel molecular pathway for sister chromatid resolution and emphasizes a role for histone chaperones in control of eukaryotic genome replication and transmission.

overall_design:
Genome-wide NAP1 and Cohesin ChIP-chip profiling in Drosophila S2 cells.
The supplementary bed file S2_cohesin_sites.bed contains cohesin binding sites obtained by intersecting the sets of significant ChIP-chip peaks for SA (a cohesin subunit; stromalin) and SMC1.

first: C

last: Verrijzer


title: H3 antibody2.S2

first: DCC

last: modENCODE

summary:
modENCODE_submission_3301
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

overall_design: 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: 13;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H3 antibody2 (target is H3)

last: Karpen

last: Elgin


title: Time-Dependent Gene Profiling Indicates the Presence of Different Phases for Ischemia/Reperfusion Injury in Retina

status: Public on Jan 24 2013

city: Louisville

first: Kalina

last: Andreeva

address: 500 S.Preston Street

institute: University of Louisville

summary: The purpose of the present study was to investigate time-dependent changes in gene expression, following induction of IR in the rat retina, and to characterize the affected pathways, networks and processes.

overall_design: 6 biological replicates with two treatments (Sham control and Ischemia reperfusion) and 3 time points (0h, 24h and 7day)

first: Nigel

last: Cooper

first: Fan

last: Wei

first: MeiXia

last: Zhang

first: Xiaohong

last: Li

first: Yinlu

last: Chen

first: Jovan

middle: D

last: Rebolledo-Mendez


title: MicroRNA-30c inhibits Human Breast Tumor Chemotherapy Resistance by regulating TWF1 and IL-11: MDA-MB231 DataSet

status: Public on Jan 18 2013

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Chemotherapy resistance frequently drives tumor progression. However, the underlying molecular mechanisms are poorly characterized. Epithelial-to-mesenchymal transition (EMT) has been shown to correlate with therapy resistance, but the functional link and signaling pathways remain to be elucidated. We report here that miR-30c, a human breast tumor prognostic marker, plays a pivotal role in chemo-resistance by a direct targeting of the actin-transporter TWF1, which promotes EMT. An IL-6 family member, IL-11 was identified as a secondary target of TWF1 in the miR-30c signaling pathway. Expression of miR-30c inversely correlated with IL-11 expression in clinical tumors and IL-11 correlated with relapse-free survival in breast cancer patients. Identification of a novel miRNA-mediated pathway that regulates chemo-resistance in breast cancer will facilitate the development of new management strategies.

overall_design: MDA-MB231 30c vs. MDA-MB231 scrambled

first: Aleix

last: Prat


title: Mouse ES cell differentiated with Activin

summary: To find miRNAs that involve in renal epithelial differentiation.

overall_design: Mouse ES cells, EB3 (129/Ola) were differentiated with Activin 10 ng/ml after 3 days of embryoid body formation.  Cells were harvested on day 18 of the differentiation.


title: HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster

status: Public on Dec 21 2012

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

summary: Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites.

overall_design: In total  44 samples; 2 replicates for each genotype and for each ChIP (HP1a, H3K9me2 and H3K9me3)

first: Margarida

middle: L

last: Figueiredo

first: Philge

last: Philip

first: Per

last: Stenberg


title: miRNA microarray of mouse renal tubular cell with or without TGFbeta

first: Ryuji

last: Morizane

summary: To find miRNAs that involve in renal epithelial-mesenchyal transition induced by TGFbeta

overall_design: Mouse renal tubular cell, MCT (derived from SJL H-2S mice) was stimulated by TGFbeta 3ng/ml for 72 hours. miRNA expressions were compared with control.

last: Monkawa


title: miR-34c attenuates epithelial-mesenchymal transition and renal fibrosis of kidneys with ureteral obstruction.

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Toshiaki


title: Searching for IPN-specific gene expression profiles in Salmo salar using susceptible and resistant families challenged with the Infectious Pancreatic Necrosis virus (IPNV).

status: Public on Sep 05 2012

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Infectious pancreatic necrosis (IPN) is widespread disease with global distribution and highly contagious, which leads to severe economic problems both freshwater and saltwater, particularly in the Atlantic salmon (Salmo salar). In this work we analyzed and evaluated gene expression profiles in resistant and susceptible families associated to S. salar exposed to IPNV in order to understand the defense mechanisms mounted by resistant fish in combating infection. Experimentally, 29 families with known pedigree and variability were infected by immersion with 1x106 PFU/ml of IPNV, and a gamma frailty model analysis based on Kaplan-Meier mortality curves were obtained to identify and classify families as susceptible or resistant. Samples of head kidney tissue were obtained at day 1 and 5 post-infection from susceptible and resistant families and pooled to analyse their expression pattern with realt-ime PCR and one-color salmon-specific oligonucleotide microarray (21K). The microarray results showed clear differences in both families, where resistant fish presented an over-expression of genes associated with endocrine function, and a down-regulation of genes associated principally with tissue differentiation, metabolism protein degradation, cell signaling and immunological process. Moreover qPCR analysis using as target a number of transcripts associated with immunological processes showed the same trend observing a higher expression in susceptible than resistant families, indicating significant differences for CCL-19, CCRγc, IL-12, IFN-α, and IFN-γ.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: The one-color oligonucleotide microarrays included in this study was performed using pooled samples from each families at two different post-infection time condition. In the case of susceptible families were chosen at 1 day post-infection (dpi) the families 5352 (n = 2) and 5469 (n = 2) and at 5 dpi the families 5629 (n = 2) and 5637 (n = 2), whereas in resistant families were selected at 1 dpi the families 5459 (n =3) and 5761 (n =3), and at 5 dpi the families 5463 (n =3) and 5764 (n =3).

middle: E


title: microRNA expression profiling of various C57Bl/6 myeloid cell populations

status: Public on Nov 22 2012

city: Rehovot

first: Alexander

last: Mildner

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary:
microRNAs are assumed to fine-tune cellular mRNA expression levels predisposing them for the control of cell development and cell fates. However, despite increasing appreciation of the role of miRNAs in controlling myeloid cell functions and some evidence for their contribution in in vitro monocyte differentiation, the in vivo role of specific miRNAs in the development and homeostasis of myeloid cells remains to be investigated.
Here we profiled the microRNA expression of 8 different myeloid cell population including myeloid precursors (MP), myeloid dendritic cell precursors (MDP), common dendritic cell precursors (CDP), plasmacytoid dendritic cells (PDC) and Gr1+ monocytes from the bone marrow and three different spenic denritic cells (DCs): CD4+ DCs, CD8+ DCs and CD4-CD8- DCs. The source of the cells were female C57BL/6 animals in an age of 6 weeks. The FACS isolation was done on a pooled cell suspension from a minimum of 5 animals.

overall_design: C57BL/6 mice in an age of 6 weeks were purchased from Harlan. For bone marrow (BM) precursor isolation, ACK (0.15M NH4Cl, 0.1M KHCO3, 1mM EDTA in PBS) lyzed BM cells from femur and tibia were pooled from 15 mice and enriched by MACS with biotinylated CD135 (A2F10) followed by anti-biotin MACS beads (Miltenyi). The enriched fraction was further stained with Streptavidin-PerCP, CD117 (2B8), CD115 (AFS98) and lineage antibody cocktail (CD11b (M1/70), CD3 (145-2C11), CD4 (GK1.5), CD8α (53-6.7), Gr1 (RB6-8C5), Sca-1 (D7), B220 (RA3-6B2), Ter-119, CD11c (N418), NK1.1 (PK136)). Splenic dendritic cells were pre-enriched from 8 mice by CD11c MACS beads (Miltenyi) and further stained for CD8α, CD4, CD11c and CD86 (PO3). BM plasmacytoid DCs were isolated from 5 mice, followed by Ficoll enrichment and stained for CD11c, CD317 (927) and Siglec H (eBio440c). BM monocytes were isolated from Ficoll enriched BM cells from 5 mice. Staining markers were: CD11b, Gr1 and CD115. All antibodies were purchased from BioLegend or eBioscience if not indicated otherwise. A FACSAria cytometer (Becton-Dickinson) was used for sorting and duplets were excluded by their FSC-H vs. FSC-W appearance.

first: Steffen

last: Jung


title: UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery [tiling array]

status: Public on Nov 28 2012

city: Worcester

first: Jie

last: Wang

state: MA

address: 364 Plantation St.

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: The transposon silencing piRNAs are produced from precursors that are encoded by heterochromatic clusters and processed in the perinuclear nuage. We show that the Drosophila nuclear DEAD box protein UAP56, previously implicated in mRNA splicing and nuclear export, co-localizes with the cluster-associated HP1 homologue Rhino. Prominent nuclear foci containing Rhi and UAP56 localize directly across the nuclear envelope from Vasa, a conserved DEAD box protein and core nuage component that is required for piRNA production, and piRNA precursors immunoprecipitate with both UAP56 and Vasa.   A uap56 point mutation that prevents UAP56 protein co-localization with Rhino also disrupts nuage organization, transposon silencing, and expression of dual strand piRNA clusters.  By contrast, this allele significantly increases ectopic piRNAs from protein coding genes.  We therefore propose that UAP56 and Vasa organize a piRNA-processing compartment that spans the nuclear envelope, increasing the efficiency and specificity of piRNA biogenesis.

overall_design: 3 replicates of each sample (uap56, vasa), total RNA samples hybridized to tiling array.