|
| Status |
Public on Jun 07, 2014 |
| Title |
EZH2 in NT2 cells |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Anti EZH2 ChIP from NTERA-2 cl.D1 chromatin
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: EZH2
cell line: NTERA-2 cl.D1
|
| Treatment protocol |
none
|
| Growth protocol |
NTERA-2 cl.D1 embryonic carcinoma cells (ATCC #CRL-1973, lot#4742175) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, ATCC #30-2002) supplemented with 10% of FBS (ATCC #30-2020) at 37C in 5% CO2 atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 37C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006.
|
| Label |
biotin
|
| Label protocol |
8ug of amplified ChIP product was fragmented with DNAse I and labeled with TdT by biotin-11-ddATP incorporation
|
| |
|
| Channel 2 |
| Source name |
DNA isolated from matching input NTERA-2 cl.D1 chromatin
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NTERA-2 cl.D1
chip antibody: none
|
| Treatment protocol |
none
|
| Growth protocol |
NTERA-2 cl.D1 embryonic carcinoma cells (ATCC #CRL-1973, lot#4742175) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, ATCC #30-2002) supplemented with 10% of FBS (ATCC #30-2020) at 37C in 5% CO2 atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 37C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006.
|
| Label |
biotin
|
| Label protocol |
8ug of amplified ChIP product was fragmented with DNAse I and labeled with TdT by biotin-11-ddATP incorporation
|
| |
|
| |
| Hybridization protocol |
Hybridization of labeled DNA was done in 200ul of solution containing 12xMES, 5M TMAC (Sigma, Cat# T3411), 3nM control oligo B2 (Affymetrix Cat# 900301), 1mg/ml Human Cot-1 DNA (Invitrogen Cat# 15279-011), 10mg/ml sonicated herring sperm DNA and 1% Triton X100. for 18 hours at 45C with 45rpm rotation. Staining and washing was done using EukGE-WS2v4 protocol
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
|
| Description |
EZH2 ChIP in NTERA-2 cl.D1 cells, Biological Rep 1-2
|
| Data processing |
The data was median scaled to 100 and the ratio of average ChIP to average Input was computed and smoothed by taking trimmed mean over sliding 675bp window. All operations were performed with TiMAT v2.8.3
The .sgr files were produced with TiMAT v2.8.3 and contain average ChIP/ average Input values smoothed by taking trimmed mean over sliding 675bp window. The coordinates were further converted to Hg19 (2009) genomic release using liftOver script
|
| |
|
| Submission date |
Oct 26, 2012 |
| Last update date |
Jun 08, 2014 |
| Contact name |
Yuri B Schwartz |
| Organization name |
Umeå University
|
| Street address |
Byggnad 6L, NUS
|
| City |
Umeå |
| ZIP/Postal code |
90187 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL4915 |
| Series (2) |
| GSE41853 |
Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes (Human) |
| GSE41854 |
Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes |
|
