|
| Status |
Public on May 01, 2016 |
| Title |
Conventional_XGFP-Type4_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
XGFP, type4, replicate 4
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1/ICR
cell line: trophoblast stem cell line
cell type: XGFP cells
colony type: type 4
culture medium: Conventional
|
| Growth protocol |
Conventional TSC line were cultured on mitomycin-C (Sigma-Aldrich, St. Louis, MO, USA)-treated primary MEFs in RPMI1640 medium (Thermo Fisher Scientific, San Jose, CA,USA) with 20% fetal bovine serum (Thermo Fisher Scientific), 25 ng/ml human recombinant FGF4 (Wako, Osaka, Japan), 1 ug/ml heparin (Sigma-Aldrich), 100 μM 2-mercaptoethanol 100 (2-ME) (Sigma-Aldrich), 1% Glutamax (Thermo Fisher Scientific), and 1 mM sodium pyruvate (Thermo Fisher Scientific) at 37.5 ºC in a humidified incubator with 5% CO2. Defined TSC line was cultured in CDM/FAXY medium at 37.5 ºC in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol (Life Technologies) from 30–50 TSCs clonies and subjected to linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre Biotechnologies).
|
| Label |
Cy3
|
| Label protocol |
5.0 ug of amplified RNA was labelled with Cianine-3 (Cy3) dye (GE Healthcare) for 90 minutes at RT. Labelled RNAs were purified with RNeasy MinElute kit (Qiagen) and checked with the NanoDrop ND-1000 Spectrophotometer
|
| |
|
| Hybridization protocol |
600 ng Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized at 65°C for 17 hours according to manufacturer's instructions.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in type4 colonies of XGFP cells
XGFP_Type4_4
amplified RNA
|
| Data processing |
The scanned images of microarray slides were processed using Feature Extraction software 10.5.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 12.5 (Agilent Technologies) and transformed by default setting.
Raw signal intensities were normalized by default setting of GeneSpring12.5. Normalized data expressed in log2 scale.
|
| |
|
| Submission date |
Dec 22, 2015 |
| Last update date |
May 01, 2016 |
| Contact name |
Kimiko Inoue |
| E-mail(s) |
[email protected]
|
| Organization name |
BRC, RIKEN
|
| Department |
Bioresource Engineering Division
|
| Street address |
3-1-1 Koyadai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-0074 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE76255 |
Cellular dynamics of mouse trophoblast stem cells: Identification of a persistent stem cell type. |
|
