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Series GSE17287 Query DataSets for GSE17287
Status Public on Jul 29, 2009
Title ML-DmBG3-c2 Replication Origins
Project modENCODE
Organism Drosophila melanogaster
Experiment type Other
Summary 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
 
Overall design 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
Web link http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
 
Contributor(s) MacAlpine D, MacAlpine H, DeNapoli L
Citation(s) 21177973
BioProject PRJNA63463
Submission date Jul 23, 2009
Last update date Aug 31, 2012
Contact name DCC modENCODE
E-mail(s) help@modencode.org
Phone 416-673-8579
Organization name Ontario Institute for Cancer Research
Lab modENCODE DCC
Street address MaRS Centre, South Tower, 101 College Street, Suite 800
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A3
Country Canada
 
Platforms (1)
GPL7787 Agilent_Dm_5.1_470_tiling
Samples (3)
GSM432732 ML-DmBG3-c2-R1 extraction1_array1_origin
GSM432733 ML-DmBG3-c2-R2 extraction2_array1_origin
GSM432734 ML-DmBG3-c2-R3 extraction3_array1_origin

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17287_Bg3_early_origins_MA2Cscore.wig.gz 1.4 Mb (ftp)(http) WIG
GSE17287_Bg3_early_origins_peaks.gff.gz 7.1 Kb (ftp)(http) GFF
GSE17287_RAW.tar 224.1 Mb (http)(custom) TAR (of TXT)
Processed data provided as supplementary file

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