|
| Status |
Public on Jul 24, 2010 |
| Title |
GM17109 |
| Sample type |
RNA |
| |
|
| Source name |
Lymphoblastoid cell line GM17109
|
| Organism |
Homo sapiens |
| Characteristics |
ethnic group: AA African-American
cell line (coriell id): GM17109
wei id: Wei031
cell type: EBV-transformed lymphoblastoid cells
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM17109
|
| Treatment protocol |
No treatment was used.
|
| Growth protocol |
LCLs were cultured in RPMI 1640 medium supplemented with 15% heat-inactivated Fetal Bovine Serum (FBS). According to the protocol from the Coriell website (http://ccr.coriell.org/sections/support/global/lymphoblastoid.aspx?pgid=213), LCLs were maintained at a density of 2-8 × 10^5 cells/ml, and were split or re-fed with fresh medium every three days, depending on the growth status of each cell line.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each of the cell lines using Qiagen RNeasy Mini kits (QIAGEN, Inc.). RNA quality was tested using an Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Labeling was performed according to the Affymetrix Gene Chip technical manual.
|
| |
|
| Hybridization protocol |
The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.
|
| Scan protocol |
The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.
|
| Description |
Basal gene expression level of lymphoblastoid cell line GM17109.
|
| Data processing |
The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as the normalization method.
|
| |
|
| Submission date |
Jul 23, 2010 |
| Last update date |
Sep 24, 2010 |
| Contact name |
Liewei Wang |
| E-mail(s) |
wang.liewei@mayo.edu
|
| Phone |
507-284-5264
|
| Fax |
507-284-4455
|
| URL |
http://mayoresearch.mayo.edu/staff/wang_l2.cfm
|
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology and Experimental Therapeutics
|
| Street address |
200 First street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE23120 |
Basal gene expression data from Human Variation Panel |
| GSE24277 |
Human Variation Panel: Gene Expression and Genotype |
|
