|
| Status |
Public on Sep 24, 2008 |
| Title |
04-018 gDNA, Wpa, 0.1ng, experiment ID 141565 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
0.1 ng of sample 04-018 genomic DNA, amplified using Wpa
|
| Organism |
Homo sapiens |
| Characteristics |
Genomic DNA sample originally with large-scale deletions in Cs22.
Wpa was started from 0.1 ng of the gDNA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QiaGen QIAEXII kit with the option for >4 kb DNA
|
| Label |
Cy3
|
| Label protocol |
Labeling performed by NimbleGen Inc. using NimbleGen protocol.
|
| |
|
| Channel 2 |
| Source name |
0.1 ng genomic DNA from 7 normal male individuals (Promega), amplified using Wpa
|
| Organism |
Homo sapiens |
| Characteristics |
Pooled genomic DNA from 7 normal male individuals (Promega).
Wpa was started from 0.1 ng of the gDNA.
Used as control.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QiaGen QIAEXII kit with the option for >4 kb 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 known large aberrations (Copy Number Variations). This particular array was applied for judging the possible locus-by-locus bias and distortion (if any) existed with the products resulted from the process of whole genome amplification (Wpa) with an input of the original gDNA.
|
| 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 |
|
