|
| Status |
Public on Jan 01, 2013 |
| Title |
SNF5overexpression-OCT4 ChIP seq |
| Sample type |
SRA |
| |
|
| Source name |
embryonic carcinoma NCCIT
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SNF5 overexpressed cells
ChIP: OCT4A
antibody catalog#: ab19857
antibody vendor: Abcam
|
| Treatment protocol |
We transfected the exogenous SNF5 for overexpression and harvest the cells at post 72 hrs transfection.
|
| Growth protocol |
NCCIT cells were routinely subcultured using opimal media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
CCGTCC_KEL656A75_peaks.bed: hg19
|
| |
|
| Submission date |
Feb 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
jueng soo You |
| Organization name |
USC
|
| Department |
Norris Comprehensive Cancer Center
|
| Lab |
Peter Jones
|
| Street address |
1441 Eastlake Ave
|
| City |
LA |
| State/province |
CA |
| ZIP/Postal code |
90042 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE36134 |
Genome-wide maps of chromatin remodeler SNF5 in human pluripotent cells. |
| GSE36140 |
SNF5 is an essential executor of epigenetic regulation in pluripotency and differentiation |
|
| Relations |
| SRA |
SRX123445 |
| BioSample |
SAMN00792953 |
