|
| Status |
Public on Mar 08, 2013 |
| Title |
HCT116_SSS1_rep1 |
| Sample type |
genomic |
| |
|
| Source name |
HCT116 Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell line: HCT116
cell type: colorectal carcinoma cell
treatment: M.SssI treated
|
| Treatment protocol |
2x10^5 nuclei were treated with 1x M.SssI buffer and 50U of M.SssI for 15 minutes. A no-enzyme control was included. SAHA treatment was performed for 24hours with 1uM SAHA
|
| Growth protocol |
Cells were grown under standard conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using standard phenol chloform procedures with ethanol precipitation. Zymo EZ DNA kit was used for bisulfite conversion
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina labeling protocol
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina 450k methylation array using standard Illumina protocols
|
| Scan protocol |
Beadchips were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting.
|
| Data processing |
Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. Data points were marked null if 1) Probes contained single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.05 were also replaced as Null. Furthermore, probes containing at least one null across the tumor sample set were masked as null. Beta value was calculated as M/(M+U) and were background subtracted. Detection P values were obtained using the Z-score formula as previously described (Noushmehr et al., 2010, Cancer Cell).
|
| |
|
| Submission date |
Mar 20, 2012 |
| Last update date |
Mar 08, 2013 |
| Contact name |
Kurinji Pandiyan |
| Organization name |
University of Southern California
|
| Department |
Department of Urology - Norris Comprehensive Cancer Center
|
| Street address |
1441 Eastlake Avenue NOR 7344
|
| City |
Los Angeles |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE36580 |
AcceSssIble: an array-based assay for the study of chromatin accessibility and DNA methylation using the CpG methyltransferase SssI |
| GSE38858 |
AcceSssIble Assay to Study the Chomatin Accessibility and DNA Methylation |
|
