|
| Status |
Public on Jul 30, 2013 |
| Title |
11P [aCGH] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumor_primary
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary tumor
|
| Treatment protocol |
1M, 2M, 4M, 9M, 12M received chemo while 10M received radiation.
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the tumor samples using QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).
|
| Label |
Cy5
|
| Label protocol |
The Genomic DNA ULS labeling kit for FFPE Samples (Agilent) was used to chemically label 1 mg of genomic DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) according to the manufacturer’s protocol (Agilent Technologies, Inc., Palo Alto, CA).
|
| |
|
| Channel 2 |
| Source name |
normal female - control/ reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
sample type: normal female reference DNA (control)
|
| Treatment protocol |
1M, 2M, 4M, 9M, 12M received chemo while 10M received radiation.
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the tumor samples using QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
The Genomic DNA ULS labeling kit for FFPE Samples (Agilent) was used to chemically label 1 mg of genomic DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) according to the manufacturer’s protocol (Agilent Technologies, Inc., Palo Alto, CA).
|
| |
|
| |
| Hybridization protocol |
Equimolar mixture of labeled normal and tumor DNA was applied to the Agilent Human Genome CGH 2x400k Microarray. Hybridization was carried out at 65°C for 40 hours, in a rotating oven at 20 rpm.
|
| Scan protocol |
CGH-v4_95. Feature extraction v.9.5
|
| Data processing |
The data quality of each microarray was assessed using the Quality Metrics report generated by the Agilent CGH analytics software (v.3.4). Copy number aberrations were detected using the Aberration Detection Method (ADM-1) algorithm, based on computing significance scores for all genomic intervals. Before calling any aberration the log ratios are normalized by subtracting the expected average µ from all log ratios vi, and then these modified log ratios are divided by the estimated variance σ. This transforms the log ratio scores into a normal distribution with a mean of 0 under the null model assumption.
|
| |
|
| Submission date |
Jul 29, 2013 |
| Last update date |
Jul 30, 2013 |
| Contact name |
Ramakrishna Sompallae |
| E-mail(s) |
ramakrishnas@gmail.com
|
| Phone |
319 353 5548
|
| Organization name |
University of Iowa
|
| Department |
Iowa Institute of Human Genetics
|
| Lab |
Bioinformatics
|
| Street address |
285 Newton Road, 5292 CBRB
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52240 |
| Country |
USA |
| |
|
| Platform ID |
GPL9777 |
| Series (2) |
| GSE49324 |
Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling [aCGH] |
| GSE49327 |
Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling |
|
