|
| Status |
Public on Dec 31, 2015 |
| Title |
HMEC TGFb 8 d Sss I |
| Sample type |
genomic |
| |
|
| Source name |
Human mammary epithelial cell TGFb treated 8 d, M. Sss I treat
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HMLE
time point: 8d
|
| Treatment protocol |
To induce the expression of Twist, HMLE-Twist-ER cells were exposed to 4-hydroxy tamoxifen (4-OHT) at a concentration of 20 nM continuously until change in morphology was observed, typically 12 days. TGF-beta1 at a concentration of 2.5 ng/ml was used to treat HMLE cells for 12 days.
|
| Growth protocol |
The immortalized human mammary epithelial cell line (HMLE) and the derivative cell line HMLE-Twist-ER were kindly provided by the Robert Weinberg laboratory (MIT). The culture of the cells was carried out as described previously (Elenbaas et al., 2001; Mani et al., 2008)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified by phenol/chloroform extraction and ethanol precipitation. Bisulfite conversion was performed using the EZ DNA methylation Kit (Zymo Research). All samples passed bisulfite conversion quality control and were subsequently processed for the Illumina Infinium DNA methylation platform (Human Methylation 450 Bead Chip).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation HM450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
Freshly prepared nuclei (2x10^5 cells) were resuspended in 1X M.SssI reaction buffer (NEB), then treated with 50U of M.SssI (NEB) in 15µL 10X reaction buffer, 45µL 1M sucrose and 0.75µL SAM in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20nM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight (Gal-Yam et al., 2006).
|
| Data processing |
BeadStudio software v3.2
|
| |
|
| Submission date |
Nov 17, 2014 |
| Last update date |
Dec 31, 2015 |
| Contact name |
Xiaojing Yang |
| E-mail(s) |
xiaojiny@usc.edu
|
| Phone |
(323)865-0740
|
| Organization name |
USC/Norris Comprehensive Cancer Center
|
| Street address |
1441 Eastlake Ave, Room 7336
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE63366 |
The dynamics of chromatin accessibility during EMT |
|
