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Sample GSM1099403 Query DataSets for GSM1099403
Status Public on Jun 01, 2013
Title SD27HR_d6
Sample type RNA
 
Source name WA09 embryonic stem cells, NC, day 6
Organism Homo sapiens
Characteristics cell line: WA09
cell type: embryonic stem cells
treatment: LDN-193189, SB431542, CHIR 99021
condition: NC
day of collection: 6
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 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)
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

Data table header descriptions
ID_REF
VALUE Quantile-normalized signal intensity

Data table
ID_REF VALUE
7A5 6.9068
A1BG 6.84482
A1CF 6.69629
A26C3 6.63575
A2BP1 6.55211
A2LD1 7.12557
A2M 6.49951
A2ML1 6.45624
A3GALT2 6.53558
A4GALT 7.24184
A4GNT 6.94887
AAA1 6.66889
AAAS 7.2477
AACS 7.53283
AACSL 6.67441
AADAC 6.67093
AADACL1 7.03995
AADACL2 6.67095
AADACL3 6.47097
AADACL4 6.3551

Total number of rows: 34694

Table truncated, full table size 543 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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