|
| Status |
Public on Oct 18, 2013 |
| Title |
GM12878_gDNA_HumanOmni2.5-Quad |
| Sample type |
genomic |
| |
|
| Source name |
GM12878_gDNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: Lymphoblasts
population: CEU
assayed molecule: gDNA
|
| Biomaterial provider |
CEU_LCL HapMap
|
| Treatment protocol |
DNA from the cell lysates was extracted using the GenElute DNA Miniprep Kit (SigmaAldrich, Suffolk, UK) according to the protocol provided by the manufacturer and concentrations were determined using the NanoDrop ND-1000.
|
| Growth protocol |
All cells were obtained from the Coriell Institute for Medical Research (Camden, NJ). The LCLs were grown in T75 flasks in 1X RPMI 1640 Media (invitrogen, Burlington, ON), with 2 mM L-glutamine, 15% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2. LCL cells were harvested during log growth phase. The Fibroblast primary cell lines were immortalized as previously desribed (Grundberg et al., PLoS Genet., 2011), and then grown in medium containing a-MEM (SigmaAldrich) supplemented with 2 mmol/l L-Glutamine, 100 U/mL penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2. At 70%-80% confluence, fibroblast cells were harvested.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA and gDNA were extracted from cell lysates and we applied a cDNA synthesis protocol as previously described in Moros et al., Genome Biology, 2011 (PMID: 21418647).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
according to manufacturer's instructions
|
| |
|
| Hybridization protocol |
according to manufacturer's instructions
|
| Scan protocol |
according to manufacturer's instructions
|
| Description |
CEU Pedigree #1463 - Mother
|
| Data processing |
GenomeStudio from Illumina
For convenience, data was compiled based on analysis date into 20 individual sets.
|
| |
|
| Submission date |
Sep 30, 2013 |
| Last update date |
Jan 14, 2014 |
| Contact name |
Tomi Pastinen |
| E-mail(s) |
[email protected]
|
| Organization name |
McGill University
|
| Department |
Human & Medical Genetics
|
| Street address |
740 Dr Penfield
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A0G1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13314 |
| Series (1) |
| GSE51272 |
Genome-wide characterization of allelic chromatin in human fibroblast and lymphoblastoid cell lines by high-density allele-specific analyses |
|
