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Sample GSM608139 Query DataSets for GSM608139
Status Public on Jan 02, 2011
Title Rep1-BES1
Sample type genomic
Source name ChIP DNA with anti-BES1 antibody from bes1-D seedlings
Organism Arabidopsis thaliana
Characteristics age: 2-week old seedlings
genotype: bes1-D
antibody: rabbit anti-BES1 polyclonal antibody
Growth protocol bes1-D Arabidopsis plants were grown in MS plates or soil under long day (16h light/8h dark) conditions at 22oC
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation was performed with 14-day-old bes1-D seedlings. Briefly, plant tissues were cross-linked with 1% formaldehyde for 15mins and nuclei were isolated using sucrose gradients. Chromatin was sonicated to generate fragments with the average size of 500bp and precipitated using BES1 antibody or GFP antibody (Molecular Probe) as negative control. Immunocomplexes were harvested by protein A beads, washed and reverse cross-linked by boiling in the presence of Chelex resin (Bio-Rad).
Label biotin
Label protocol 7.5ug of DNA from each sample was fragmentated and terminally labelled with the GeneChip® WT (Whole Transcript) Double-Stranded DNA Terminal Labeling Kit following the product manual
Hybridization protocol 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit.Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.
Scan protocol Arrays were scanned on an Affymetrix Scanner 3000
Description ChIP with anti-BES1 antibody from biological replicate 1
Data processing Log2-transformed signal intensity data was quantile normalized with the cisgenome software and stored in BAR files (combined in "BES1_ChIP_normalization.txt" for all samples).
Submission date Oct 13, 2010
Last update date Sep 04, 2019
Contact name Xiaofei Yu
Phone 515-294-4816
Organization name Iowa state Univeristy
Street address 1035D Roy J Carver Co-Lab
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
Platform ID GPL10977
Series (1)
GSE24684 Genome-wide mapping of BES1 binding sites in Arabidopsis thaliana
Reanalyzed by GSE136843

Supplementary file Size Download File type/resource
GSM608139.CEL.gz 25.2 Mb (ftp)(http) CEL 15.7 Mb (ftp)(http) BAR
Processed data provided as supplementary file
Processed data are available on Series record

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