ModENCODE RNA-Seq of Drosophila cell lines Kc167, CME_W1_Cl.8+, S2-DRSC and ML-DmBG3-c2
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE15596 | GEO | 2009/04/08
REPOSITORIES: GEO
Similar Datasets
Project description:Deep Sequencing of mRNA from the Drosophila melanogaster cell lines Kc167, CME_W1_Cl.8+, S2-DRSC and ML-DmBG3-c2. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Analysis of poly(A)+ RNA from 2 biological replicates of Kc167, CME_W1_Cl.8+, S2-DRSC and ML-DmBG3-c2 cell lines.
2009-04-08 | E-GEOD-15596 | biostudies-arrayexpress
Project description:The changes in transcript titers are described for Drosophila ML-DmBG3-c2 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response
2009-03-20 | GSE11069 | GEO
Project description:modENCODE_submission_711 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Early origins of replication were identified by treating cells with hydroxyurea (HU), a potent inhibitor of nucleotide synthesis, in the presence of the nucleotide analogue BrdU. Treatment of synchronized ML-DmBG3-c2 cells with HU stalls replication forks and activates the intra S-phase checkpoint, thereby limiting BrdU incorporation to those sequences mmediately adjacent to early activating replication origins. BrdU enriched sequences surrounding early origins of replication are then enriched by immunoprecipitation with an anti-BrdU antibody. Early origins are then detected by hybridization to Agilent genomic tiling arrays. Peaks are called using MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Genotype: y v f mal; Sex: Unknown NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2
2010-05-15 | E-GEOD-17287 | biostudies-arrayexpress
Project description:modENCODE_submission_2553 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Analysis of copy number variation across modENCODE Drosophila cell line by high throughput sequencing. We observe numerous copy number variations for the different cell lines, with each cell line having a distinct ploidy signature. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: deep sequencing analysis EXPERIMENT TYPE: deep sequencing analysis. 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; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2
2010-01-21 | E-GEOD-19958 | biostudies-arrayexpress
Project description:modENCODE_submission_670 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains. Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Genotype: y v f mal; Sex: Unknown NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2
2009-07-29 | E-GEOD-17281 | biostudies-arrayexpress
Project description:modENCODE_submission_711 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Early origins of replication were identified by treating cells with hydroxyurea (HU), a potent inhibitor of nucleotide synthesis, in the presence of the nucleotide analogue BrdU. Treatment of synchronized ML-DmBG3-c2 cells with HU stalls replication forks and activates the intra S-phase checkpoint, thereby limiting BrdU incorporation to those sequences mmediately adjacent to early activating replication origins. BrdU enriched sequences surrounding early origins of replication are then enriched by immunoprecipitation with an anti-BrdU antibody. Early origins are then detected by hybridization to Agilent genomic tiling arrays. Peaks are called using MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2009-07-29 | GSE17287 | GEO
Project description:PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmBG3-c2 cells by hybridization of ChIP products with tiling microarrays.
2010-01-08 | GSE18100 | GEO
Project description:modENCODE_submission_2754 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: CHIP-seq EXPERIMENT TYPE: CHIP-seq. 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; EXPERIMENTAL FACTORS: Antibody dORC2
2010-03-16 | E-GEOD-20888 | biostudies-arrayexpress
Project description:The changes in transcript titers are described for Drosophila ML-DmBG3-c2 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
2009-03-19 | E-GEOD-11069 | biostudies-arrayexpress
Project description:Deep Sequencing of S2-DRSC small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2009-09-10 | GSE18041 | GEO