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Sample GSM4552324 Query DataSets for GSM4552324
Status Public on May 27, 2020
Title Control immunoprecipitation, biological rep 1
Sample type genomic
 
Source name no-antibody-rep1
Organism Arabidopsis thaliana
Characteristics treatment: IP without antibody
tissue: embryonic culture tissue
genotype/variation: expressing ABI3-10x-cmyc
Treatment protocol Tissue was fixed in MC buffer (10 mM potassium phosphate pH 7, 50 mM NaCl, 0.1 M sucrose) with 1% formaldehyde for one hour on ice under vacuum. The reaction was quenched with addition of cold glycine to 0.125 M and incubation on ice continued 10-30 min, after which the tissue was washed with cold MC buffer and flash frozen.
Growth protocol An embryonic culture was derived from zygotic Arabidopsis embryos that constitutively express AGL15. The test culture also has proABI3:ABI3-c-myc in the abi3-5 mutant background. The culture was grown on MS media supplemented with 10 g L-1 sucrose, 0.5 g L-1 MES and 7 g L-1 agar (pH 5.6-5.7) with kanamycin and/or hygromycin and maintained at 23°C to 24°C with a 23-h-light/1-h-dark regime.
Extracted molecule genomic DNA
Extraction protocol ChIP was performed as in Wang and Perry, 2013, Plant Physiology 161:1251-1264 using c-myc antibody
Label biotin
Label protocol Samples (7.5 microgram of DNA) were processed following the Affymetrix protocol to fragment and biotin label
 
Hybridization protocol The UK Microarray core facility performed the hybridization and scan using the Affymetrix hybridization kit
Scan protocol Affymetrix Scanner 3000 7G
Description nonspecific DNA
Data processing Normalization was using quantile in CisGenome
 
Submission date May 14, 2020
Last update date May 27, 2020
Contact name Sharyn E Perry
E-mail(s) sperr2@uky.edu
Phone 859-218-0732
Organization name University of Kentucky
Department Plant and Soil Sciences
Street address 1405 Veterans Dr.
City Lexington
State/province KY
ZIP/Postal code 40546-0312
Country USA
 
Platform ID GPL10977
Series (2)
GSE150559 Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [ChIP-chip]
GSE150561 Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites

Supplementary file Size Download File type/resource
GSM4552324_control1_070213_At35b_MR_v04_.CEL.bar.gz 16.8 Mb (ftp)(http) BAR
GSM4552324_control1_070213_At35b_MR_v04_.CEL.bar.txt.gz 18.2 Mb (ftp)(http) TXT
GSM4552324_control1_070213_At35b_MR_v04_.CEL.gz 28.6 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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