|
| Status |
Public on Dec 01, 2010 |
| Title |
303 SNP BJ38M |
| Sample type |
genomic |
| |
|
| Source name |
NHF PD38 MSRE
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary foreskin fibroblasts PD38
gender: male
|
| Treatment protocol |
DNA methylation: One microgram of genomic DNA was digested at 37oC for16 hrs with a methylation sensitive restriction enzyme (MSRE) cocktail including AciI (20 units), BsaHI (1.3 units), HhaI (2.5 units), HpaII (2.5 units), and HpyCH4IV (10 units) (NewEngland Biolabs), in a 50 microliter reaction volume with 0.1 mg/ml BSA and 10% NEB buffer #4 (New England Biolabs), ethanol precipitated, and resuspended in TE at 50 ng/µl. Replication timing: none.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA samples were extracted using the QIAamp blood mini kit (Qiagene.com).
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix).
|
| |
|
| Hybridization protocol |
As per manufacturer (Affymetrix).
|
| Scan protocol |
As per manufacturer (Affymetrix).
|
| Description |
NHF PD38 MSRE
|
| Data processing |
See reference (Aran et al 2010).
DNA methylation: Cel files of MSRE-treated and untreated DNA samples from various tissues and cell lines, hybridized to Affymetrix SNP mapping microarrays. BED files with methylation score calculated as the 1-log2 of the hybridization intensities before/after MSRE treatment are added. Replication timing: Cel files of G1 and early-S fractions of the cell cycle, obtained from exponentially grown EBV-transformed lymphocytes, hybridized to Affymetrix SNP mapping microarrays. Bed file corresponding this calculation is added.
|
| |
|
| Submission date |
Oct 27, 2010 |
| Last update date |
Dec 01, 2010 |
| Contact name |
Asaf Hellman |
| E-mail(s) |
asafh@ekmd.huji.ac.il
|
| Phone |
972-2-6758476
|
| Fax |
972-2-6758243
|
| Organization name |
Hebrew University
|
| Department |
Developmental Biology and Cancer Research
|
| Street address |
Hadassah Medical School
|
| City |
Jerusalem |
| ZIP/Postal code |
91120 |
| Country |
Israel |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE24947 |
Genome-wide connection between DNA methylation and DNA replication timing |
|
