|
| 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 |
