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Sample GSM591470 Query DataSets for GSM591470
Status Public on May 19, 2011
Title EB Rad21-GFP ChIP
Sample type SRA
 
Source name EB
Organism Mus musculus
Characteristics cell type: R1/E-derived EB
differentiation day: 12
chip antibody: goat-anti-eGFP, raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP
antibody manufacturer: generated by the Antibody and Protein purification facility of MPI-CBG
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 Chromatin IP against GFP
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 SRX026524
BioSample SAMN00110677
Named Annotation GSM591470_EB_Rad21.peaks.bed.gz
Named Annotation GSM591470_EB_Rad21.bed.gz
Named Annotation GSM591470_EB_Rad21.summits.bed.gz

Supplementary file Size Download File type/resource
GSM591470_EB_Rad21.bed.gz 54.8 Mb (ftp)(http) BED
GSM591470_EB_Rad21.peaks.bed.gz 159.9 Kb (ftp)(http) BED
GSM591470_EB_Rad21.summits.bed.gz 119.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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