|
| Status |
Public on Jul 03, 2013 |
| Title |
HRP1-1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MeDIP DNA from HRP1, replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
medip antibody: anti-5-methyl-cytosine
medip antibody vendor: Diagenode
medip antibody lot#: D004
medip antibody catalog#: mcg-611-005
|
| Treatment protocol |
HRP1 cells are established cell line
|
| Growth protocol |
cells were maintained in DMEM(HG) with 10% FCS and penicillin and streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol
|
| Label |
Cy5
|
| Label protocol |
1 µg IP DNA was directly labeled by Klenow random priming with Cy5 and input DNA was labeled with Cy3 using a NimbleGen Dual-Color DNA Labeling Kit.
|
| |
|
| Channel 2 |
| Source name |
input DNA from HRP1
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: none (input DNA)
|
| Treatment protocol |
HRP1 cells are established cell line
|
| Growth protocol |
cells were maintained in DMEM(HG) with 10% FCS and penicillin and streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol
|
| Label |
Cy3
|
| Label protocol |
1 µg IP DNA was directly labeled by Klenow random priming with Cy5 and input DNA was labeled with Cy3 using a NimbleGen Dual-Color DNA Labeling Kit.
|
| |
|
| |
| Hybridization protocol |
Labeled samples were hybridized at 42˚C for 16-20h.
|
| Scan protocol |
Arrays were scaned using the MS 200 Microarray Scanner and the MS 200 Data Collection Software
|
| Description |
subclones of Huh7 cells permissive for HCV replication
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan DNA methylation data extraction.
|
| |
|
| Submission date |
Sep 07, 2011 |
| Last update date |
Jul 03, 2013 |
| Contact name |
Qiuyue Chen |
| E-mail(s) |
chenqiuyue23@gmail.com
|
| Phone |
(214) 648-3078
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Molecular Genetics
|
| Lab |
Jin Ye
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL14546 |
| Series (2) |
| GSE31960 |
Huh7 cells exist as a mixed population of cells with distinct patterns of gene methylation |
| GSE31962 |
HCV Replication: permissive and non-permissive cells |
|
