|
| Status |
Public on Dec 18, 2018 |
| Title |
Slide3_Array1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
tumour stage: Advanced PCa
|
| Treatment protocol |
Samples were thawed to room temperature and vortexed prior to extraction.
|
| Growth protocol |
Genomic DNA was extracted from peripheral blood of human PCa and BPH subjects and were stored in EDTA tubes in -80°C freezer until use.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted from whole blood samples using QiAmp DNA Blood Mini Kit (Qiagen, Hilden, Germany). The direct method was used for sample preparation prior to labelling according to manufacturer's protocol.
|
| Label |
Cy5
|
| Label protocol |
5 μL of Random Primer was added to each reaction tube containing 26 μL of gDNA to make a total volume of 31 μL. Samples are centrifuged in a centrifuge for 1 minute at 6,000 × g. 19 μL of Labeling Master Mix was added to each reaction tube to make a total volume 50 μL. Samples were then subjected to clean-up process by adding 430 μL of 1× TE (pH 8.0), Molecular grade to each reaction tube. After discarding the flow-through, this step is repeated by adding 480 μL of 1× TE (pH 8.0), Molecular grade to each column. Upon adding 1× TE (pH 8.0), Molecular grade, 1.5 μL of each sample is tested for yield and specific activity/ degree of labeling.
|
| |
|
| Channel 2 |
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
prostate condition: BPH
|
| Treatment protocol |
Samples were thawed to room temperature and vortexed prior to extraction.
|
| Growth protocol |
Genomic DNA was extracted from peripheral blood of human PCa and BPH subjects and were stored in EDTA tubes in -80°C freezer until use.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted from whole blood samples using QiAmp DNA Blood Mini Kit (Qiagen, Hilden, Germany). The direct method was used for sample preparation prior to labelling according to manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
5 μL of Random Primer was added to each reaction tube containing 26 μL of gDNA to make a total volume of 31 μL. Samples are centrifuged in a centrifuge for 1 minute at 6,000 × g. 19 μL of Labeling Master Mix was added to each reaction tube to make a total volume 50 μL. Samples were then subjected to clean-up process by adding 430 μL of 1× TE (pH 8.0), Molecular grade to each reaction tube. After discarding the flow-through, this step is repeated by adding 480 μL of 1× TE (pH 8.0), Molecular grade to each column. Upon adding 1× TE (pH 8.0), Molecular grade, 1.5 μL of each sample is tested for yield and specific activity/ degree of labeling.
|
| |
|
| |
| Hybridization protocol |
1,350 μL of DNase/RNase-free distilled water was added to the vial containing lyophilized 10× aCGH Blocking Agent (included in the Oligo aCGH/ChIP-on-chip Hybridization Kit) to prepare 10x blocking agent. 245 μL of sample after yield-testing and addition of hybridization master mix were then hybridized following manufacturer's protocol.
|
| Scan protocol |
Scanning was done using the Agilent Technologies Scanner G2505C US81403231 by selecting Protocol CGH_107_Sep09.
|
| Data processing |
Scanned images derived from the SurePrint Scanner were extracted using Agilent Feature Extraction for Cytogenomics Software, version 2.7.8.0 (Agilent Technologies, USA) using the CGH_107_Sep09 protocol and CGH_QCMT_Sep09 metric set for background subtraction and normalization. Extracted data were analysed using the Agilent Cytogenomics Software, version 2.7 (Agilent Technologies).
|
| |
|
| Submission date |
Mar 18, 2016 |
| Last update date |
Dec 18, 2018 |
| Contact name |
Prevathe Poniah |
| Organization name |
University of Malaya
|
| Department |
Pharmacology
|
| Lab |
Pharmacogenomics
|
| Street address |
Lembah Pantai
|
| City |
Wilayah Persekutuan Kuala Lumpur |
| ZIP/Postal code |
50603 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL10154 |
| Series (1) |
| GSE79402 |
CNV Identification: Prostate Cancer (PCa) vs Benign Prostatic Hyperplasia (BPH) Human DNA Samples |
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