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Series GSE19654 Query DataSets for GSE19654
Status Public on Jun 14, 2010
Title INTACT method for gene expression and chromatin profiling of individual cell types within a tissue
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by genome tiling array
Expression profiling by genome tiling array
Summary We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis.

Keywords: Chromatin affinity-purification on microarray
Overall design All experiments were done using two channels per chip. Two types of experiments were performed. Expression profiling was performed by comparing cDNAs synthesized from nuclear RNA isolated from INTACT-prepared Arabidopsis nuclei to total sonicated genomic DNA isolated from Arabidopsis plants. Chromatin profiling was performed using INTACT-prepared Arabidopsis nuclei. DNA isolated by Chromatin immunoprecipitation (ChIP) using antibodies to modified histones was compared to histone H3 ChIP DNA from the same sample.
Contributor(s) Henikoff S, Deal RB
Citation(s) 20627084
Submission date Dec 24, 2009
Last update date Apr 18, 2012
Contact name Jorja Henikoff
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)
GPL7143 Nimblegen_HD2_Arabidopsis
Samples (16)
GSM490202 ADF_EXP_1_(294548)
GSM490203 ADF_EXP_2_(294543)
GSM490204 ADF_K27_1_(294548-2)
BioProject PRJNA122553

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
GSE19654_INTACT_ChIP_protocol.pdf.gz 36.8 Kb (ftp)(http) PDF
GSE19654_RAW.tar 1.7 Gb (http)(custom) TAR (of BEDGRAPH, DAT, GFF, PAIR)
Processed data included within Sample table
Processed data provided as supplementary file

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