Dataset mE_Replication_Timing_S2-DRSC

General Information
Name	mE_Replication_Timing_S2-DRSC	Species	D. melanogaster
Dataset type	genomic sequence profile	FlyBase ID	FBlc0000198
Source & Content
Consists of	Genomic distribution profiled by ChIP-chip. (Eaton et al., 2010.12.17)
Created by	modENCODE: Origins of Replication Group
Available from	Not available as reagents.
Strain
Stage & tissue

Cell Line	S2-DRSC
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	Replication timing was profiled genome-wide in S2-DRSC cells; early- and late-replicating DNA pulse labeled with 5-bromo-2-deoxyuridine (BrdU) at different times after release from cell cycle arrest; relative BrdU enrichment in early- versus late-pulse labeled samples was determined by comparative hybridization to genomic tiling array. (Eaton et al., 2010.12.17)
Parent collections
Component collection(s)
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	Cells were split to a density of 1.5E6 cells/ml. For labeling of early-replicating DNA, cells were arrested for 3 hours in 1mM hydroxyurea, then BrdU was added and cells were incubated for an additional 21 hours; after 24 hours, cells were resuspended in hydroxyurea-free medium and labeled with BrdU for another hour. For labeling late-replicating DNA, cells were treated for 24 hours with 1mM hydroxyurea, grown 4 hours in hydroxyurea-free medium, then grown another 2 hours in the presence of BrdU. The 'early' and 'late' labeled cells were frozen, and DNA was isolated using Proteinase K, phenol/chloroform, RNaseA and ethanol precipitation. (Eaton et al., 2010.12.17)
Collection preparation	DNA was sheared and BrdU-labeled DNA was immunoprecipitated using a purified mouse monoclonal antibody (clone 3D4). Purified immunoprecipitated DNA from 'early' and 'late' cells was fluorescently labeled using Sequenase and hybridized to genomic tiling array as per Agilent recommendations. (Eaton et al., 2010.12.17)
Mode of assay	ChIP-chip. (Eaton et al., 2010.12.17)
Assay platform	Agilent_Dm_5.1_470_tiling (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL7787) (Eaton et al., 2010.12.17)
Data analysis	Normalized and averaged data was quantile normalized between different experiments and smoothed using the Lowess function to generate a replication timing curve. (Eaton et al., 2010.12.17)
Additional data
	More information is available under: GEO: GSE17280 modMine: modENCODE_669
Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	GSE17280 mE_Replication_Timing_S2-DRSC modENCODE_669 replication timing profile (Eaton et al., 2010.12.17) S2 Replication Timing
Secondary FlyBase IDs

References ( 2 )
Research paper	Eaton et al., 2011, Genome Res. 21(2): 164--174 Chromatin signatures of the Drosophila replication program. [FBrf0213065]
Personal communication to FlyBase	Eaton et al., 2010.12.17, Incorporation of modENCODE Replication Origins Data into FlyBase. Incorporation of modENCODE Replication Origins Data into FlyBase. [FBrf0212681]