|
| Status |
Public on Sep 30, 2007 |
| Title |
HEPG; ATCC; DnaseI enriched E_070809_05_DS7809_W D |
| Sample type |
genomic |
| |
|
| Source name |
HEPG; ATCC; DnaseI enriched
|
| Organism |
Homo sapiens |
| Characteristics |
HEPG; ATCC
|
| Growth protocol |
(follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI
|
| Label |
biotin
|
| Label protocol |
Fragments were cleaned using Qiagen PCR columns. Samples were amplified using the Sigma WGA amplification kit. Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase. (See Affymetrix Chip Chip protocol)
|
| |
|
| Hybridization protocol |
Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays. Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.
|
| Scan protocol |
Arrays were scanned using an Affymetrix GeneChip Scanner 3000.
|
| Description |
Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.
DnaseI enriched
|
| Data processing |
Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software; linearly scaled to intesity of 500, 2-sided upper quantile normalization. BED files contain Log2 ratio of experimental normalized to control (2-sided Upper and linearly scaled to intensity 500) using the Affymetrix Tiling Analysis Software (TAS) version 1.1.02).
|
| |
|
| Submission date |
Sep 05, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
John A Stamatoyannopoulos |
| E-mail(s) |
jstam@altius.org
|
| Organization name |
Altius Institute / University of Washington
|
| Department |
Genome Sciences
|
| Lab |
Stamatoyannopoulos
|
| Street address |
2211 Elliott Avenue, 6th Floor
|
| City |
SEATTLE |
| State/province |
WA |
| ZIP/Postal code |
98121 |
| Country |
USA |
| |
|
| Platform ID |
GPL4913 |
| Series (1) |
| GSE8962 |
Tissue/Cell DNaseI sensitivity/hypersensitivity screening |
|
