|
| Status |
Public on Oct 01, 2015 |
| Title |
CVS [14S0010337] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Miscarriage_CVS
|
| Organism |
Homo sapiens |
| Characteristics |
sample origin: Miscarriage
clinical indication: Miscarriage
tissue: Chorionic villus sampling (CVS)
|
| Treatment protocol |
Samples were untreated
|
| Growth protocol |
Uncultured samples of chorionic villus sampling, amniotic fluid, placental tissue and blood were used for direct DNA extraction
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction done by Qiagen DNeasy® Blood & Tissue Kit following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Three costumized aCGH approach have different procedure for DNA fragmentation and labelling; Agilent-022023:1 µg of Genomic DNA samples were fragmented. The fragmented DNA sample were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-068656:300 ng of Genomic DNA samples were heat fragmented. The fragmented DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-035130:300 ng of Genomic DNA samples were enzyme digested. The digested DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.
|
| |
|
| Channel 2 |
| Source name |
control_blood
|
| Organism |
Homo sapiens |
| Characteristics |
sample origin: Healthy Chinese adult control
tissue: blood
|
| Treatment protocol |
Samples were untreated
|
| Growth protocol |
Uncultured samples of chorionic villus sampling, amniotic fluid, placental tissue and blood were used for direct DNA extraction
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction done by Qiagen DNeasy® Blood & Tissue Kit following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Three costumized aCGH approach have different procedure for DNA fragmentation and labelling; Agilent-022023:1 µg of Genomic DNA samples were fragmented. The fragmented DNA sample were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-068656:300 ng of Genomic DNA samples were heat fragmented. The fragmented DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-035130:300 ng of Genomic DNA samples were enzyme digested. The digested DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.
|
| |
|
| |
| Hybridization protocol |
After clean up and QC check, Cy3 and Cy5 labeled DNA samples were mixed together with Cot-1 DNA, blocking agent and hybridization buffer using Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit according to manufacturer's protocol. Samples were hybridized on array for 24 hours at 65oC. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2505C scanner.
|
| Data processing |
Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction
Dye was normalized automatically according to the dye norm list in eArray generating the normalized log10 ratio (Cy5/Cy3), representing test/reference
|
| |
|
| Submission date |
Sep 10, 2015 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Zirui DONG |
| E-mail(s) |
elvisdong@link.cuhk.edu.hk
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
Dept. of Obstetrics and Gynaecology
|
| Street address |
Shatin, N.T.
|
| City |
Hong Kong |
| ZIP/Postal code |
999077 |
| Country |
China |
| |
|
| Platform ID |
GPL20897 |
| Series (2) |
| GSE72891 |
aCGH for CNV detection in clinical samples |
| GSE73191 |
Chromosomal microarray data for validation of copy-number variants detection from a low-coverage whole-genome sequencing approach in clinical samples |
|
