|
| Status |
Public on Nov 30, 2015 |
| Title |
Patient 3 [Agilent] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
blood from patient 3
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: Lynch Syndrome (LS)
tissue: blood
gender: female
patient id: SL-3
|
| Growth protocol |
Not applicable.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Gentra Puregene Blood Kit (Qiagen, Valencia, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Standard Agilent protocol. Test samples have been labeled with Cy3 and controls with Cy5.
|
| |
|
| Channel 2 |
| Source name |
pooled normal reference DNA (Promega)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
gender: female
sample type: reference
|
| Growth protocol |
Not applicable.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Gentra Puregene Blood Kit (Qiagen, Valencia, CA, USA).
|
| Label |
Cy5
|
| Label protocol |
Standard Agilent protocol. Test samples have been labeled with Cy3 and controls with Cy5.
|
| |
|
| |
| Hybridization protocol |
Standard Agilent Protocol. Labeled test and control samples were mixed and hybridized into a 4x 180K slide (Agilent Product Number - G4449A).
|
| Scan protocol |
The slides were scanned on an Agilent G2565B scanner (Agilent).
|
| Description |
Patient sample Cy3-labeled mixed with reference sample Cy5-labeled.
|
| Data processing |
Data were extracted using the Agilent Feature Extraction software (v 8.5.1.1) and analyzed using the Agilent CytoGenomics software (v 3.0.1.1) with the following parameters: ADM-2 algorithm, threshold of 6.0, at least four altered probes, log2 ratio > 0.35 for gains and < -0.35 for losses. The fuzzy zero correction was applied, with a detailed visual analysis being performed for all alterations, excluding regions with poor data quality.
|
| |
|
| Submission date |
Sep 02, 2015 |
| Last update date |
Nov 30, 2015 |
| Contact name |
Rolando Andre Rios Villacis |
| E-mail(s) |
rolando.andre@unb.br
|
| Phone |
+5561996912223
|
| Organization name |
University of BrasÃlia - UnB
|
| Department |
Genetics and Morphology
|
| Lab |
Genetic Toxicology
|
| Street address |
Asa Norte
|
| City |
BrasÃlia |
| State/province |
DF |
| ZIP/Postal code |
70910-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL10150 |
| Series (2) |
| GSE72665 |
Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes [Agilent] |
| GSE72668 |
Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes |
|
