|
| Status |
Public on Jun 21, 2023 |
| Title |
ssI-C2 |
| Sample type |
genomic |
| |
|
| Source name |
H1 hESC clone with ssI at MLH1 promoter CGI
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: pluripotent stem cell line
integration of cpg free insert: Y
dna methylation at target cgi: Y
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified from cells using Qiagen DNeasy Kit according to standard instructions
[bisulfite conversion protocol] The non-methylated cytosine residues of the purified genomic DNA sample were converted into uracil using EZ DNA Methylation Kit from Zymo Research (Irvine, CA).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
We followed the standard Infinium HD Methylation protocol guide and all reagents, which were required in the procedure, were purchased from the Illumina (San Diego, CA).
|
| |
|
| Hybridization protocol |
The bisulfite converted DNAs were denatured by the 0.1N NaOH and amplified for 20 – 24 hours in the 37C hybridization chamber to produce a sufficient amount of the DNA sample. The amplified DNAs were enzymatically fragmented on the 37C heat block for 1 hour and were precipitated for 30 min at 4C. For the hybridizing the DNAs onto Illumina beadchips, the precipitated DNAs were resuspended by RA1 solution according to the manufacturer protocol and the suspended DNAs with an appropriate volume were loaded onto the Inf Methyl EPIC 8 sample beadchip (San Diego, CA). The hybridication was performed for over the 16 hours within 24 hours.
|
| Scan protocol |
The image acquisition was carried out using the Illumina iScan System (San Diego, CA).
|
| Description |
21609_M-15
Processed data file: 202139520099.igv
850 beadchip
|
| Data processing |
Raw data were processed and normalized by "SWAN" method using Bioconductor package "lumi".
The *igv processed data files represent SWAN-normalized Average Beta values.
|
| |
|
| Submission date |
Aug 07, 2022 |
| Last update date |
Jun 21, 2023 |
| Contact name |
wei chen |
| E-mail(s) |
weichen2@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Cancer Biology-BRI
|
| Street address |
1500 E Duarte Rd
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL23976 |
| Series (1) |
| GSE210680 |
Engineering Pluripotent DNA Methylation by CpG Island Methylation Response (CIMR) to Synthetic CpG-free ssDNA Insertion |
|
