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Series GSE19788 Query DataSets for GSE19788
Status Public on May 27, 2010
Title CATCH-IT method for measuring nucleosome turnover
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Direct measurement of nucleosome turnover dynamics by using co-translational incorporation of the methionine (Met) surrogate azidohomoalaine (Aha) into proteins and subsequent ligation of biotin to Aha-containing proteins through the [3+2] cycloaddition reaction between the azide group of Aha and an alkyne linked to biotin. To measure turnover rates, we treat cells briefly with Aha, couple biotin to nucleosomes containing newly incorporated histones, affinity purify with strepavidin, wash stringently to remove non-histone proteins and H2A/H2B dimers, and analyze the affinity-purified DNA using tiling microarrays. We call this strategy 'CATCH-IT' for Covalent Attachment of Tags to Capture Histones and Identify Turnover.

Keywords: Chromatin affinity-purification on microarray
 
Overall design All experiments were done using strepavidin pulldown DNA cohybridized with total input DNA to the same array. Two channels per array, Cy5 and Cy3, were used in each experiment.
 
Contributor(s) Henikoff S, Deal RB
Citation(s) 20508129
Submission date Jan 07, 2010
Last update date May 29, 2013
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platforms (1)
GPL6888 Henikoff_Dmel_r52_ChIP tiling design
Samples (12)
GSM494304 AHA_3hr_1_(3C_382774)
GSM494305 AHA_3hr_2_(CSB_277840-3)
GSM494306 AHA_6hr_1_(AHA_cy5-cy3_284230)
Relations
BioProject PRJNA121809

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
GSE19788_CATCH-IT_protocol.pdf.gz 56.4 Kb (ftp)(http) PDF
GSE19788_RAW.tar 1.4 Gb (http)(custom) TAR (of BEDGRAPH, GFF, PAIR)
Processed data included within Sample table
Processed data provided as supplementary file

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