|
| Status |
Public on Sep 26, 2011 |
| Title |
SYTSSX2_FLAG_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
SYTSSX2_FLAG_ChIP
|
| Organism |
Mus musculus |
| Characteristics |
cell type: SYTSSX2-expressing C2C12 myoblasts
chip antibody: anti-FLAG antibody (Sigma)
|
| Treatment protocol |
Cells were infected with retrovirus carrying SYTSSX2 expression vector for 6h, then medium was changed to fresh growth medium. Cells were allowed to grow for 48 hours post-infection before chromatin immunoprecipitation.
|
| Growth protocol |
Cells were maintained in DMEM containing 10% FBS, 1% penicillin/streptomycin at 37˚C, 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed according to previously described methods (Boyer LA et al, 2005. Cell 122:947-56) with some modifications using either control IgG (Abcam) or anti-FLAG (Sigma) antibodies. The purified ChIP DNA was further sonicated prior to end repair, addition of 'A' base to DNA fragment 3' ends, and ligation of adaptors using Illumina ChIPSeq DNA sample prep kit. Ligated DNA samples were gel purified and amplified by PCR. PCR products were purified and diluted to 10nM for cluster generation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The Illumina Analysis Pipeline was used for image analysis and base calling to generate fastq sequence files.
Bowtie (Langmead B et al, 2009. Genome Biol 10:R25) was used to align the sequences to the mouse genome. The files generated by Bowtie were used as input for Model-based Analysis of ChIPSeq (MACS) (Zhang Y et al, 2008. Genome Biol 9:R137) which was used to identify peaks.
|
| |
|
| Submission date |
Jan 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Josiane Eid |
| E-mail(s) |
josiane.eid@vanderbilt.edu
|
| Organization name |
Vanderbilt University
|
| Street address |
2220 Pierce Avenue
|
| City |
Nashville |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE26564 |
Genomewide occupancy of the synovial sarcoma-associated SYT-SSX2 oncoprotein in C2C12 myoblasts |
| GSE26565 |
Reprogramming of mesenchymal stem cells by the synovial sarcoma-associated oncogene SYT-SSX2 |
|
| Relations |
| SRA |
SRX037908 |
| BioSample |
SAMN00190761 |
