|
| Status |
Public on Jun 01, 2013 |
| Title |
SD28_d0 |
| Sample type |
RNA |
| |
|
| Source name |
WA09 embryonic stem cells, day 0
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WA09
cell type: embryonic stem cells
treatment: LDN-193189, SB431542
day of collection: 0
|
| Treatment protocol |
hESCs were plated on matrigel for differentiation and grown in the presence of 100 nM LDN-193189 (Stemgent) and 10 uM SB431542 (Tocris) for DSi, or grown in the presence of 100 nM LDN-193189, 10 uM SB431542, and 3 uM CHIR 99021 (Stemgent) for NC, or 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.
|
| Growth protocol |
hESCs (WA09; passages 32-50) were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2. hESCs were grown in DMEM:F12 hESC media containing 6ng/mL FGF2 and passaged using dispase or accutase.
|
| 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 3.
|
| 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) |
| GSE45223 |
Genome-wide analysis of differential gene expression in human embryonic stem cell-derived central nervous system, neural crest, and progenitor populations over time |
| GSE45227 |
Genome-wide analysis of gene expression in melanocytes derived from human embryonic stem cells and patient specific induced pluripotent stem cells |
|
