|
| Status |
Public on Jan 10, 2008 |
| Title |
No Ab Spike in DNA sample diluted ENCODE NimbleGen hg17 tiling array (92003) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Spike in DNA sample
|
| Organism |
Homo sapiens |
| Characteristics |
Spike in DNA sample amplified by LM-PCR
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Spike in DNA
|
| Label |
Cy5
|
| Label protocol |
Cy5
|
| |
|
| Channel 2 |
| Source name |
Control DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Control DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Control DNA
|
| Label |
Cy3
|
| Label protocol |
Cy3
|
| |
|
| |
| Hybridization protocol |
NimbleGen hybridization protocol
|
| Scan protocol |
NimbleGen scan protocol
|
| Description |
Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.
|
| Data processing |
log2R normalized using the limma R package method=loess
|
| |
|
| Submission date |
Nov 27, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Department |
Department of Cellular and Molecular Medicine
|
| Lab |
Laboratory of Gene Regulation
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0653 |
| Country |
USA |
| |
|
| Platform ID |
GPL4559 |
| Series (2) |
| GSE10112 |
Systematic evaluation of variability in simulated ChIP-chip experiments |
| GSE10114 |
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets |
|
