|
| Status |
Public on Jan 01, 2014 |
| Title |
H3_ChIP_ 4hpi |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
KSHV-infected SLK Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SLK
hrs post kshv infection: 4
antibody: H3
|
| Treatment protocol |
SLK cells were de novo infected by spin-infection (2,000 rpm, 45 min at 30°C) using MOI 1. After infection, the medium was changed and the infected cells were harvested at the indicated time points.
|
| Growth protocol |
SLK cells were maintained in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin (P/S).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP and Input DNA samples were prepared according to previously published protocols Toth, Z. et al. Epigenetic analysis of KSHV latent and lytic genomes. PLoS pathogens 6:e1001013, 2010).
|
| Label |
Cy5
|
| Label protocol |
1.3 µg of ChIP or Input DNA were labeled according to the manufacturer's protocol (Agilent ChIP-on-chip Analysis, version 11.0).
|
| |
|
| Channel 2 |
| Source name |
KSHV-infected SLK Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SLK
hrs post kshv infection: 4
antibody: none
|
| Treatment protocol |
SLK cells were de novo infected by spin-infection (2,000 rpm, 45 min at 30°C) using MOI 1. After infection, the medium was changed and the infected cells were harvested at the indicated time points.
|
| Growth protocol |
SLK cells were maintained in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin (P/S).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP and Input DNA samples were prepared according to previously published protocols Toth, Z. et al. Epigenetic analysis of KSHV latent and lytic genomes. PLoS pathogens 6:e1001013, 2010).
|
| Label |
Cy3
|
| Label protocol |
1.3 µg of ChIP or Input DNA were labeled according to the manufacturer's protocol (Agilent ChIP-on-chip Analysis, version 11.0).
|
| |
|
| |
| Hybridization protocol |
Microarrays were hybridized in a hybridization over for 24 hours at 65C and 20 RPM. The arrays were washed and scanned in an ozone-free tent.
|
| Scan protocol |
Scanned on an Agilent G2539CA scanner.
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1) with the feature extraction protocol for ChIP-chip experiments (ChIP_107_Sep09).
|
| Data processing |
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Oct 24, 2013 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Clifford G. Tepper |
| E-mail(s) |
[email protected]
|
| Phone |
916-734-7195
|
| Organization name |
UC Davis School of Medicine
|
| Department |
Biochemistry and Molecular Medicine
|
| Street address |
4645 2nd Avenue, Room 2300A
|
| City |
Sacramento |
| State/province |
CA |
| ZIP/Postal code |
95817 |
| Country |
USA |
| |
|
| Platform ID |
GPL17838 |
| Series (1) |
| GSE51660 |
Biphasic euchromatin-to-heterochromatin transition on the KSHV genome following de novo infection |
|
