|
| Status |
Public on Apr 17, 2014 |
| Title |
#1_undiff_24hr_compl |
| Sample type |
RNA |
| |
|
| Source name |
undifferentiated human ES_complete medium for 24hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: khES3
cell type: undifferentiated human ES cells
culture medium: complete medium
culture duration: 24 hrs
|
| Treatment protocol |
khES3 cells are cultured in the presence or abesence of extracellular methionine for 5 or 24 hr (#1_undiff_5hr_compl, #1_undiff_5hr_deltaMet, #1_undiff_24hr_compl, #1_undiff_24hr_deltaMet). 0hr indicates khES3 cells just before these manipulations (#1_undiff_0hr).
|
| Growth protocol |
Before the following assay, human embryonic stem cells (khES3) are grown in human ES media to 70-80% confluent. Endoderm cells are prepared by directed-differentiation of khES3 with activinA (#1_Endoderm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extraced using RNeasy Mini Kit, according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Expression Kit User Manual, P/N 702646 Rev. 8, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
1_undiff_24hr_compl
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
|
| |
|
| Submission date |
Feb 24, 2014 |
| Last update date |
Apr 19, 2014 |
| Contact name |
nobuaki shiraki |
| E-mail(s) |
shiraki@bio.titech.ac.jp
|
| Phone |
81-45-924-5814
|
| Organization name |
Tokyo Institute of Technology
|
| Department |
School of Life Science and Technology
|
| Street address |
4259-B-25 Nagatsuta-cho, Midori-ku
|
| City |
Yokohama |
| ZIP/Postal code |
226-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE55283 |
Expression data from undifferentiated human ES cell line, khES3, grown using complete or methionine deprived media and ES cell derived endoderm |
| GSE55285 |
Expression data from undifferentiated human ES cell line, khES3, grown using complete, methionine, leucine or lysine deprived media and ES cell derived endoderm |
|
