|
| Status |
Public on Dec 28, 2007 |
| Title |
HOXA13 ChIP (HG18 Array 1 of 2) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
HOXA13 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
primary human foreskin firbroblasts
|
| Treatment protocol |
NO additional treatments were performed
|
| Growth protocol |
Foreskin firbroblasts were grown in DMEM with 10% Fetal Bovine Serum until confluent and growth arrested in G0 by serum starvation for 48 hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA and was amplified by sigma WGA2 kit for 1 round of amplification
|
| Label |
CY3
|
| Label protocol |
Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension
|
| |
|
| Channel 2 |
| Source name |
Mock ChIP of Rabbit IGG
|
| Organism |
Homo sapiens |
| Characteristics |
Human primary foreskin fibroblasts
|
| Treatment protocol |
NO additional treatments were performed
|
| Growth protocol |
Foreskin firbroblasts were grown in DMEM with 10% Fetal Bovine Serum until confluent and growth arrested in G0 by serum starvation for 48 hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA and was amplified by sigma WGA2 kit for 1 round of amplification
|
| Label |
CY5
|
| Label protocol |
Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension
|
| |
|
| |
| Hybridization protocol |
Standard Nimblegen hybridization kits and protocols were used
|
| Scan protocol |
Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols
|
| Description |
HG18 Array 1 of 2
|
| Data processing |
Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction
|
| |
|
| Submission date |
Dec 27, 2007 |
| Last update date |
Dec 27, 2007 |
| Contact name |
John Louis Rinn |
| E-mail(s) |
jrinn@broad.mit.edu
|
| Phone |
6505752491
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Chang Lab
|
| Street address |
2155 CCSR 269 Campus Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL6325 |
| Series (1) |
| GSE9922 |
HOXA13 Chromatin Immunoprecipitation on human HG18 Nimblegen 2 array promoter set |
|
