|
| Status |
Public on Feb 20, 2008 |
| Title |
K562 crosslinked mononucleosome (repeat1) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
K562 mononucleosome crosslinked, MNase-digested
|
| Organism |
Homo sapiens |
| Characteristics |
53 year old female derived chronic myuelogenous leukemia cells; human K562
|
| Treatment protocol |
Cells were grown untreated and were centrifuged for harvesting.
|
| Growth protocol |
Cells were grown in suspension in RPMI media with 10% fetal bovine calf serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
see manuscript
|
| Label |
biotin
|
| Label protocol |
Nimblegen ChIP labeling protocol (http://www.nimblegen.com)
|
| |
|
| Channel 2 |
| Source name |
K562 bare genomic crosslinked, MNase-digested
|
| Organism |
Homo sapiens |
| Characteristics |
53 year old female derived chronic myuelogenous leukemia cells; human K562
|
| Treatment protocol |
Cells were grown untreated and were centrifuged for harvesting.
|
| Growth protocol |
Cells were grown in suspension in RPMI media with 10% fetal bovine calf serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
see manuscript
|
| Label |
biotin
|
| Label protocol |
Nimblegen ChIP labeling protocol (http://www.nimblegen.com)
|
| |
|
| |
| Hybridization protocol |
Nimblegen Hybridization protocol (http://www.nimblegen.com)
|
| Scan protocol |
Arrays were scanned using AXON 5uM scanner
|
| Description |
MNase-digested crosslinked chromatinized DNA compared with MNase-digested bare-genomic DNA for nucleosome mapping.
|
| Data processing |
Calculated log2 intensity ratios from raw intensity values
|
| |
|
| Submission date |
Dec 28, 2007 |
| Last update date |
Feb 05, 2008 |
| Contact name |
Peter Kharchenko |
| Organization name |
Harvard Medical School
|
| Department |
DBMI
|
| Lab |
Kharchenko
|
| Street address |
10 Shattuck St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL5790 |
| Series (1) |
| GSE10042 |
Stable nucleosome positions in HOX clusters; human K562 and HeLa cells |
|
