|
| Status |
Public on Dec 28, 2007 |
| Title |
ENCODE Spike-In, Yale Group Sample 2 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
ENCODE Spike, Undiluted
|
| Organism |
Homo sapiens |
| Characteristics |
Cloned promoter sequences
|
| Extracted molecule |
other |
| Extraction protocol |
Sample received as part of the ENCODE consortium "ENCODE Spike 77 ng/ul, Undiluted"
|
| Label |
Cy5
|
| Label protocol |
5 ug DNA was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
|
| |
|
| Channel 2 |
| Source name |
Control for ENCODE Spike
|
| Organism |
Homo sapiens |
| Characteristics |
Sheared genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sample received as part of the ENCODE consortium "ENCODE Control 200 ng/ul"
|
| Label |
Cy3
|
| Label protocol |
5 ug DNA was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
|
| |
|
| |
| Hybridization protocol |
The labeled simulated "ChIP DNA" was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).
|
| Scan protocol |
Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
|
| Description |
Red Channel: "ENCODE spike", 5 ug
Green Channel: "ENCODE control", 5 ug
|
| Data processing |
value = log_2(Signal for Cy5 / Signal for Cy3)
|
| |
|
| Submission date |
Dec 21, 2007 |
| Last update date |
Dec 26, 2007 |
| Contact name |
Guoneng Zhong |
| E-mail(s) |
guoneng.zhong@yale.edu
|
| Organization name |
Yale Med
|
| Street address |
300 George St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL2131 |
| Series (2) |
| GSE10004 |
ENCODE Spike-In, Yale Group |
| GSE10114 |
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets |
|
