|
| Status |
Public on Mar 01, 2010 |
| Title |
Reference HapMap sample NA12249_C5 |
| Sample type |
genomic |
| |
|
| Source name |
Reference HapMap sample NA12249_C5
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: reference HapMap
cell line: NA12249_C5
gender: female
|
| Treatment protocol |
None
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cell samples were harvested in each collaborative laboratorion, washed with PBS and sent as a frozen cell pellet to analysis laboratory. Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen)
|
| Label |
TdT
|
| Label protocol |
accordingly manufactures protocol
|
| |
|
| Hybridization protocol |
accordingly manufactures protocol
|
| Scan protocol |
accordingly manufactures protocol
|
| Description |
Hybridized in Finnish DNA Microarray Centre
|
| Data processing |
For detecting copy number variation in the samples, we utilized Affymetrix Genotyping Console 3.0.1 and Birdseed v2-algorithm. Samples were normalized against 40 International HapMap samples for copy number variation (CNV), Loss of heterozygosity (LOH) and Single nucleotide polymorphism (SNP).
|
| |
|
| Submission date |
Mar 04, 2009 |
| Last update date |
Jan 29, 2010 |
| Contact name |
Elisa Maarit Närvä |
| E-mail(s) |
elisa.narva@btk.fi
|
| Organization name |
University of Turku
|
| Department |
Turku Centre for Biotechnology
|
| Lab |
Riitta Lahesmaa
|
| Street address |
Tykistönkatu 6
|
| City |
Turku |
| ZIP/Postal code |
20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE15096 |
Affymetrix SNP 6.0 array data for human embryonic stem cell lines |
| GSE15097 |
High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines |
|
