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Status |
Public on Jun 01, 2013 |
Title |
SD26HR_d3 |
Sample type |
RNA |
|
|
Source name |
WA09 embryonic stem cells, NC, day 3
|
Organism |
Homo sapiens |
Characteristics |
cell line: WA09 cell type: embryonic stem cells treatment: LDN-193189, SB431542, CHIR 99021 condition: NC day of collection: 3
|
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.
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|
|
Hybridization protocol |
Standard Illumina hybridization protocol.
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Scan protocol |
Standard Illumina scanning protocol.
|
Description |
Replicate 1.
|
Data processing |
The data were normalised using quantile normalisation in Partek Genomics Suite software.
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|
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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 |
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