|
| Status |
Public on Mar 31, 2011 |
| Title |
HCT116 MIRA |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
methylated DNA fraction enriched by MIRA. DNA was isolated from HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colon cancer cell
cell line: HCT116
genotype/variation: HCT116
enrichment procedure: MIRA
antibody vendor/catalog number: In Lab purified His-MBD3L1 & GST-MBD2b
|
| Treatment protocol |
no treatment
|
| Growth protocol |
cells were cultured in McCoy’s 5A medium with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For UMC, sonicated DNA was treated according to the manufacturer’s instructions for the UMC kit (Active Motif), purified and amplified by using LM-PCR. For ChIP-chip experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by 0.125 M glycine. 8 µg of sonicated chromatin was incubated with appropriate antibodies overnight and captured with A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR.
|
| Label |
Cy5
|
| Label protocol |
According to standard NimbleGen Protocol
|
| |
|
| Channel 2 |
| Source name |
Input DNA from HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colon cancer cell
cell line: HCT116
genotype/variation: HCT116
enrichment procedure: none, Input
|
| Treatment protocol |
no treatment
|
| Growth protocol |
cells were cultured in McCoy’s 5A medium with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For UMC, sonicated DNA was treated according to the manufacturer’s instructions for the UMC kit (Active Motif), purified and amplified by using LM-PCR. For ChIP-chip experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by 0.125 M glycine. 8 µg of sonicated chromatin was incubated with appropriate antibodies overnight and captured with A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR.
|
| Label |
Cy3
|
| Label protocol |
According to standard NimbleGen Protocol
|
| |
|
| |
| Hybridization protocol |
According to NimbleGen Kit
|
| Scan protocol |
Follow NimbleScan's default using Agilent Scanner
|
| Description |
HCT116 MIRA
|
| Data processing |
Cy5/Cy3 log2 ratio scaled by NimbleScan software v2.5 with Tukey Biweight mean
|
| |
|
| Submission date |
Dec 14, 2010 |
| Last update date |
Mar 31, 2011 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL11313 |
| Series (2) |
| GSE26020 |
Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription |
| GSE26040 |
Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks |
|
