|
| Status |
Public on Sep 24, 2008 |
| Title |
04-018 vs. 04-018 gDNA (self), experiment ID 47750 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Genomic DNA for sample 04-018
|
| Organism |
Homo sapiens |
| Characteristics |
Genomic DNA sample with large-scale deletions in Cs22.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard protocol for genomic DNA.
|
| Label |
Cy3
|
| Label protocol |
Labeling performed by NimbleGen Inc. using NimbleGen protocol.
|
| |
|
| Channel 2 |
| Source name |
Genomic DNA for sample 04-018
|
| Organism |
Homo sapiens |
| Characteristics |
Genomic DNA sample with large-scale deletions in Cs22.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard protocol for genomic DNA.
|
| Label |
Cy5
|
| Label protocol |
Labeling performed by NimbleGen Inc. using NimbleGen protocol.
|
| |
|
| |
| Hybridization protocol |
Hybridization performed by NimbleGen Inc. using NimbleGen protocol.
|
| Scan protocol |
Scan performed by NimbleGen Inc. using NimbleGen protocol and NimbleScan software.
|
| Description |
HR-CGH was performed in order to demonstrate the detectability of the breakpoints and size of large aberrations (Copy Number Variations). This particular array was accomplished to show the ratio of a DNA sample against itself on array, which was to demonstrate the variability/noise of the array hybridization itself. Theoretically the ratio should be 1 (or log2 ratio = 0).
|
| Data processing |
The data were processed in genomic region bins of a number of varying sizes. Using NimbleScan software, data were qspline-normalized. The normalized data, representing log2 (test/reference) ratios, are provided in the .gff files.
|
| |
|
| Submission date |
Sep 09, 2008 |
| Last update date |
Jan 04, 2012 |
| Contact name |
Xinghua Pan |
| E-mail(s) |
xinghua.pan@yale.edu
|
| Phone |
203-7372616
|
| Organization name |
Yale University School of Medicine
|
| Department |
Department of Genetics
|
| Lab |
Sherman Weissman
|
| Street address |
300 Cedar Street, TAC-S320
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
CT |
| Country |
USA |
| |
|
| Platform ID |
GPL3448 |
| Series (2) |
| GSE12731 |
Evaluation of the amplicons for detection of known CNVs using Cs22 HR-CGH |
| GSE12751 |
Evaluation of Wpa-generated amplicons for SNP typing (allele bias), locus bias, and detection of known CNVs |
|
