|
| Status |
Public on Oct 31, 2012 |
| Title |
ESC UNDIFF LINE BG03 PASSAGE 54 |
| Sample type |
genomic |
| |
|
| Source name |
ESC UNDIFF LINE BG03 PASSAGE 54
|
| Organism |
Homo sapiens |
| Characteristics |
class: ESC
condition: UNDIFF
cell line: BG03
passage: 54
gender: MALE
|
| Growth protocol |
All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human pluripotent stem cells were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. Pluripotent stem cells were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer’s instructions.
|
| Label |
Alexa555 and Alexa647
|
| Label protocol |
As per manufacturer (Illumina)
|
| |
|
| Hybridization protocol |
DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.
|
| Scan protocol |
The BeadChip arrays were scanned using the BeadArray Reader (Illumina).
|
| Description |
ESC UNDIFF LINE BG03 PASSAGE 54
SAMPLE_5
|
| Data processing |
The scanned data files were processed by BeadStudio (Illumina). BeadStudio was also used to calculate the Log R ratio and B allele frequency using a cluster file (Human1M-Duov3_B.egt) supplied by Illumina.
|
| |
|
| Submission date |
Jan 17, 2012 |
| Last update date |
Oct 31, 2012 |
| Contact name |
Kory R Johnson |
| E-mail(s) |
[email protected]
|
| Phone |
301-402-1956
|
| Organization name |
NINDS/NIH
|
| Department |
DIR IT & Bioinformatics
|
| Lab |
Bioinformatics Section
|
| Street address |
10/3B01, 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6984 |
| Series (2) |
| GSE34200 |
The NIH Human Pluripotent Stem Cell Database |
| GSE35157 |
The NIH Human Pluripotent Stem Cell Database (Illumina, snp) |
|
