Paired End CNV Kc 167
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: DCC modENCODE
PROVIDER: E-GEOD-41346 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:modENCODE_submission_5526 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 sequencing replication intermediates that were differentially labeled with BrdU during S-phase progression. Briefly, cells were pulse labeled with BrdU and sorted into early, middle and late S-phase fractions. BrdU labeled sequences from each fraction of S-phase were enriched by immunoprecipitation and sequenced on the Illumina platform. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: read length (base pair) ; Cell Line Kc167; read length (base pair)
2012-10-04 | E-GEOD-41349 | biostudies-arrayexpress
Project description:modENCODE_submission_5524 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 EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line S2-DRSC
2012-10-04 | E-GEOD-41347 | biostudies-arrayexpress
Project description:modENCODE_submission_5525 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 EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+
2012-10-04 | E-GEOD-41348 | biostudies-arrayexpress
Project description:modENCODE_submission_5527 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 sequencing replication intermediates that were differentially labeled with BrdU during S-phase progression. Briefly, cells were pulse labeled with BrdU and sorted into early, middle and late S-phase fractions. BrdU labeled sequences from each fraction of S-phase were enriched by immunoprecipitation and sequenced on the Illumina platform. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: read length (base pair) ; Cell Line S2-DRSC; read length (base pair)
2012-10-04 | E-GEOD-41350 | biostudies-arrayexpress
Project description:modENCODE_submission_5528 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 sequencing replication intermediates that were differentially labeled with BrdU during S-phase progression. Briefly, cells were pulse labeled with BrdU and sorted into early, middle and late S-phase fractions. BrdU labeled sequences from each fraction of S-phase were enriched by immunoprecipitation and sequenced on the Illumina platform. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: 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: read length (base pair) ; Cell Line ML-DmBG3-c2
2012-10-04 | E-GEOD-41351 | biostudies-arrayexpress
Project description:modENCODE_submission_2552 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: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: Cell Line Kc167
2010-01-21 | E-GEOD-19957 | biostudies-arrayexpress
Project description:modENCODE_submission_2755 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: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: Antibody dORC2
2010-03-16 | E-GEOD-20889 | biostudies-arrayexpress
Project description:modENCODE_submission_2783 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: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: Antibody Pan MCM2-7 Antibody
2010-03-16 | E-GEOD-20890 | biostudies-arrayexpress
Project description:modENCODE_submission_3201 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 EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+ In this experiment, there is no ChIP step. Simply separate the polytene dna from the tissue (cell line) and seq them, if more reads (than other regions) then they are the CNV regions. Two independent samples were merged to generate the single wiggle file.
2011-03-23 | E-GEOD-28136 | biostudies-arrayexpress
Project description:modENCODE_submission_3009 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 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: 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 H3K9acS10P (new abcam lot) (target is H3K9acS10P)
2010-11-18 | E-GEOD-25363 | biostudies-arrayexpress