|
| Status |
Public on Jan 13, 2010 |
| Title |
Japanese Female, NA18972, slide 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Immortalized cell line, Japanese female
|
| Organism |
Homo sapiens |
| Characteristics |
population: Japanese
gender: female
sample_name: NA18972
sample source: HapMap
sample type: test
|
| Treatment protocol |
Not treated.
|
| Growth protocol |
Cell lines were cultured under 10% FBS+standard RPMI media. No antibacterials were used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Gentra DNA extraction kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
1.5ul of genomic DNA fragmented and amplified using random primer. Cy3-dCTP and Cy5-dCTP were incorporated using the BioPrime DNA labelling kit using the manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
NA10851 reference
|
| Organism |
Homo sapiens |
| Characteristics |
population: Caucasian
gender: male
sample_name: NA10851
sample source: HapMap
sample type: reference
|
| Treatment protocol |
Not treated.
|
| Growth protocol |
Cell lines were cultured under 10% FBS+standard RPMI media. No antibacterials were used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Gentra DNA extraction kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
1.5ul of genomic DNA fragmented and amplified using random primer. Cy3-dCTP and Cy5-dCTP were incorporated using the BioPrime DNA labelling kit using the manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed using wash buffer I, II (Agilent Inc.).
|
| Scan protocol |
Scanned on an Agilent G2505 Scanner.
|
| Description |
CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.
|
| Data processing |
Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Jan 10, 2010 |
| Last update date |
Jan 13, 2010 |
| Contact name |
Dongwan Hong |
| E-mail(s) |
[email protected]
|
| Phone |
+82-2-740-8424
|
| Fax |
+82-2-741-5423
|
| URL |
http://www.gmi.ac.kr
|
| Organization name |
Genomic Medicine Institute, Seoul National University College of Medicine
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
28 Yeongeon-dong, Jongno-gu
|
| City |
Seoul |
| ZIP/Postal code |
110-799 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL9859 |
| Series (1) |
| GSE19651 |
Discovery of common Asian copy number variants using high-resolution array CGH |
|
