|
| Status |
Public on Apr 01, 2012 |
| Title |
Cybrid from haplogroup F, biological rep 1, technical rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
Cybrid clone with mtDNA from person 1 in haplogroup F
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cybrid clone
mtdna from: person 1
mtdna haplogroup: F
|
| Treatment protocol |
Cybrid clones from three mtDNA haplogroups were generated as follows. Platelets from twelve persons from three mtDNA haplogroups were separated from whole blood by centrifugation and fusion was carried out by mixing rho0 cells with platelets in a 1:1 ratio and then centrifuging at 1,500g for 15 miniutes. DMEM was removed and the cells were resuspended in 0.8 ml of 50% (v/v) polyethylene glycol (Signam-Aldrich). Sixty seconds after fusion, the cells were resuspended in DMEM and left to recover at 37 degree Celcius for 45 minutes. 24 fours after fusion, the medium was replaced with DMEM lacking uridine to select against unfused cells.
|
| Growth protocol |
The rho0 cell was obtained after long-term exposure of osteoscarcoma cell line to ethidium bromide (50ng/ml) and was grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 mg/ml 5-bromodeoxyuridine (BrdU), 50 ug/ml uridine, and 10% fetal bovine serum (FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation of total RNA from cells was performed using Rneasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Targets were prepared by using the GeneChip Whole Transcript Sense Target Labeling Assay (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The prepared targets were hybridized to GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
GeneChips were scanned using Scanner 3000 7G (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions.
|
| Description |
Gene expression data from cybrid clone F-1
F-1-1
|
| Data processing |
The CEL files were imported to Affymetrix Expression Console software and normalized by RMA (Robust Multi-chip Average) method and log2 transformed.
|
| |
|
| Submission date |
Dec 21, 2010 |
| Last update date |
Apr 01, 2012 |
| Contact name |
Seungwoo Hwang |
| E-mail(s) |
[email protected]
|
| Phone |
82-42-879-8544
|
| Organization name |
Korea Research Institute of Bioscience and Biotechnology
|
| Department |
Korean Bioinformation Center
|
| Street address |
52 Eoeun-dong Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE26244 |
Expression data from cytoplasmic hybrid (cybrid) and rho0 cells |
|
