|
| Status |
Public on Jan 31, 2010 |
| Title |
FAIRE performed in human pancreatic islet cells, sample 1 (ENCODE regions) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
FAIRE processed DNA from pancreatic islets
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Human pancreatic islet chromatin crosslinked with 1% formaldehyde solution for 10 min and then sheared by sonication.
cell type: pancreatic islet
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted using phenol-chloroform
|
| Label |
Cy5
|
| Label protocol |
Sample labeled by incorporation of cyanine dyes by polymerization with Klenow fragment primed by random nonomers
|
| |
|
| Channel 2 |
| Source name |
Input DNA from pancreatic islets
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Human pancreatic islet DNA sheared by sonication.
cell type: pancreatic islet
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted using phenol-chloroform
|
| Label |
Cy3
|
| Label protocol |
Sample labeled by incorporation of cyanine dyes by polymerization with Klenow fragment primed by random nonomers
|
| |
|
| |
| Hybridization protocol |
Hybridizations were performed in a MAUI hybridization station for 16 h at 42°C
|
| Scan protocol |
Arrays were scanned with an Axon Scanner 4000B
|
| Description |
Samples were amplified using ligation mediated (LM) PCR.
|
| Data processing |
log2 ratios of Cy5/Cy3 normalized so that the mean ratio is 0
|
| |
|
| Submission date |
Jan 14, 2010 |
| Last update date |
Jan 28, 2010 |
| Contact name |
Kyle Jeffrie Gaulton |
| Organization name |
UCSD
|
| Department |
Pediatrics
|
| Street address |
9500 Gilman Drive
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL3514 |
| Series (1) |
| GSE17616 |
A map of open chromatin in human pancreatic islets |
|
