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Sample GSM1183114 Query DataSets for GSM1183114
Status Public on Nov 24, 2014
Title bioTip60
Sample type SRA
 
Source name bioTip60 ChIP DNA from ES cells
Organism Mus musculus
Characteristics strain background: 129/Sv
cell line: J1
cell type: mouse embryonic stem cells
genotype/variation: expressing Flag-bio tagged Tip60
chip beads: Dynabeads MyOne Streptavidin T1
chip beads vendor: Invitrogen
chip beads cat. #: #65601
Growth protocol Mouse J1 ES cell lines cultured on gelatin coated plates were maintained as described previously (Kim et al., 2008). Briefly, cells were maintained in DMEM (Dulbecco's modified Eagle's medium) supplemented with 15% fetal calf serum, 0.1 mM β-mercaptoethanol, 2 mM L-glutamine, 0.1 mM nonessential amino acid, 1% of nucleoside mix (100× stock, Sigma), 1000 U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and 50 U/ml Penicillin/Streptomycin.
Extracted molecule genomic DNA
Extraction protocol The Flag-bio tagged mouse ES cells were fixed in 1% formaldehyde for 7 minutes at room temperature. The formaldehyde was quenched using 2.5M glycine before harvest for extract preparation. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with size of 500-800bp were immunoprecipitated using Streptavidin beads (Dynabeads MyOne Streptavidin T1), and 2% SDS was applied for one of the washing steps.
massive parallel sequencing (bioChIP-Seq)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1000
 
Description bioTip60 ChIP DNA from ES cells
Data processing Sequences were aligned using the software Bowtie (Langmead et al., 2009) into July 2007 assembly of the mouse genome (mm9, NCBI Build 37). For the identification of DBP bound peaks, software MACS 1.4.2 (Zhang et al., 2008) were used with dynamic local lambda calculation and building shifting model under P-value cutoff at 1e-5.
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: WIG file generated from software MACS 1.4.2 (Zhang et al., 2008)
 
Submission date Jul 10, 2013
Last update date May 15, 2019
Contact name Jonghwan Kim
E-mail(s) jybella@utexas.edu
Phone 512-232-8046
Organization name University of Texas at Austin
Department Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology
Lab Kim Lab
Street address 2506 Speedway NMS 4.246
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL15103
Series (1)
GSE48666 CpG island-mediated global gene regulatory modes in mouse embryonic stem cells
Relations
BioSample SAMN02230367
SRA SRX319553

Supplementary file Size Download File type/resource
GSM1183114_bioTip60.wig.gz 57.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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