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Sample GSM591472 Query DataSets for GSM591472
Status Public on May 19, 2011
Title EB Rad21-GFP IgG
Sample type SRA
 
Source name EB
Organism Mus musculus
Characteristics cell type: R1/E-derived EB
differentiation day: 12
chip antibody: Goat IgG isotype control
antibody manufacturer: Jackson Immunoresearch
antibody lot number: 76310
antibody catalog number: 005-000-003
Treatment protocol 30mio. cells were crosslinked with formaldehyde at 1% final concentration, lysates were sonicated to average fragment size of 500bp, IP was performed with 5ug antibody
Growth protocol Maintained on Gelatine-coated dishes in DMEM (GLUTAMAX high-glucose, Gibco) media supplemented with 15% FBS (Gibco), 0.055mM b-mercaptoethanol (Gibco), 1x MEM non-essential amino acids (Invitrogen), 5000u/ml penicillin-streptomycin (Invitrogen) and 50uM LIF
Extracted molecule genomic DNA
Extraction protocol 20ng of the immunoprecipitated DNA was used to generate the ChIP-seq library according to the manufacture’s protocol (Illumina) and sequenced with the Genome Analyzer II (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description input DNA
Data processing Alignment: Sequence reads were obtained and mapped to the mouse m37 genome assembly (mm9; July 2007) using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
 
Submission date Sep 08, 2010
Last update date May 15, 2019
Contact name Maciej Paszkowski-Rogacz
Organization name Technische Universität Dresden
Department UCC / Medical Faculty and University Hospital Carl Gustav Carus
Lab Medical Systems Biology (Prof. Buchholz)
Street address Tatzberg 47/49
City Dresden
ZIP/Postal code 01307
Country Germany
 
Platform ID GPL9250
Series (2)
GSE24029 Genome-wide maps of Rad21 in R1/E embryonic stem cells and R1/E derived Embryoid bodies
GSE24030 The Cohesin Complex Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity
Relations
SRA SRX026526
BioSample SAMN00110679

Supplementary file Size Download File type/resource
GSM591472_EB_IgG.bed.gz 48.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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