|
| Status |
Public on Jun 22, 2016 |
| Title |
TKZP4 |
| Sample type |
RNA |
| |
|
| Source name |
fibroblast-derived iPS cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: induced pluripotent stem cells
|
| Treatment protocol |
The cells were collected by picking up clumps manually.
|
| Growth protocol |
All cells were cultured on irradiated mouse embryonic fibroblasts in standard human pluripotent stem cell media with basic fibroblast growth factor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from semi-confluent cells using RNeasy mini kit (Quiagen).
|
| Label |
Cy3
|
| Label protocol |
cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.
|
| |
|
| Submission date |
Mar 31, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Takafumi Hiramoto |
| E-mail(s) |
takafumiester@gmail.com
|
| Organization name |
University of Washington
|
| Department |
Division of Hematology
|
| Street address |
1959 NE Pacific Street, HSB K-260
|
| City |
Seattle |
| ZIP/Postal code |
98195-7720 |
| Country |
USA |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE79759 |
Human embryonic stem cells vs. fibroblast-derived iPS cells |
| GSE79762 |
New non-transmissible measles virus vector for establishment of iPS cells |
|
| Relations |
| Reanalyzed by |
GSE113533 |
