|
| Status |
Public on Jun 01, 2013 |
| Title |
SD27_d0_b |
| Sample type |
RNA |
| |
|
| Source name |
WA09 embryonic stem cells, WT, day 0
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WA09
cell type: embryonic stem cells (ESCs)
cell stage: ESC
genotype: WT
day of collection/passage: day 0
clone: SD27
|
| Treatment protocol |
hESCs were plated on matrigel for differentiation and grown in the presence of 100 nM LDN-193189, 10 uM SB431542, 3 uM CHIR 99021 (Stemgent), 25 ng/ml BMP4 (R&D) and 100nM EDN3 (American Peptide Company) for BE. Cells were dissociated at day 11 and replated on poly-ornithine-, laminin-, and fibronectin-coated plates in NB/Mel media. NB/Mel media was prepared by replacing the WNT3A-CM component in Mel-1 media (Fang et al., 2006) with Neurobasal (Invitrogen) medium containing 2% B27 supplement (Invitrogen), 3μM Chir, 25 ng/ml BMP4, and 500 μM dbcAMP. Cells were fed every other day and passaged weekly for maintenance and expansion.
|
| Growth protocol |
hESCs (WA09; passages 32-50) were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2. hESC cells were grown in DMEM:F12 hESC media containing 6ng/mL FGF2 and passaged using dispase or accutase. Primary melanocytes were maintained in M254 media with HMGS supplement (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with an Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol.
|
| Scan protocol |
Standard Illumina scanning protocol.
|
| Description |
Replicate 2.
|
| Data processing |
The data were normalised using quantile normalisation in Partek Genomics Suite software.
|
| |
|
| Submission date |
Mar 15, 2013 |
| Last update date |
Jun 01, 2013 |
| Contact name |
Yvonne Mica |
| E-mail(s) |
grubery@mskcc.org
|
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL10904 |
| Series (2) |
| GSE45226 |
Genome-wide analysis of gene expression in human pluripotent stem cell-derived melanocyte progenitors, mature melanocytes, and disease-specific melanocytes |
| GSE45227 |
Genome-wide analysis of gene expression in melanocytes derived from human embryonic stem cells and patient specific induced pluripotent stem cells |
|
