|
| Status |
Public on Mar 18, 2013 |
| Title |
fibroblast cell line rep3 |
| Sample type |
RNA |
| |
|
| Source name |
fibroblast cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: TSKM-iPS mouse derived fibroblast cells (3-days induced)
stage or passages: p4
strain: OG2-GFP/Rosa26-M2rtTA
|
| Treatment protocol |
The cells were cultured until the appropriate stage. The culture medium were threw out and washed with PBS. The cells were centrifuge dissociated by 0.05% trypsin EDTA.The ESCs were added 2-folds-volume ESM and dissociated to single cells. The cell suspension were plated in new dished for 0.5hr(37℃) to clear away the feeder cells. The supernatant supension were further collected carefully and centrifuged for RNA extraction. The fibroblasts were centrifuged to collect the cells and treated with centrifuge centrifuged and treated with Trizol (Invirtrogen).
|
| Growth protocol |
The iPS cells were cultured on mitomycin C treated MEFs in ES medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 15% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF. The TSKM 2nd induction cells were deriven from TSKM iPS mice and cultured with Feeder Medium for 3 passages. On passages 4 the culture were changed to ES Medium with doxycycline for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.(Invirtrogen)
|
| Label |
biotin
|
| Label protocol |
WT Terminal Labeling Kit (Affymetrix.Inc)
|
| |
|
| Hybridization protocol |
Hybridization, wash and Stain Kit(Affymetrix.Inc)
|
| Scan protocol |
GeneChip® Scanner 3000 7G 3000 (Affymetrix.Inc)
|
| Data processing |
The raw image files were processed by Bioconductor “Affy” and “vsn” package, the intensity of probes in arrays passed quality control were calculated and normalized for expression value.
|
| |
|
| Submission date |
Jul 25, 2012 |
| Last update date |
Mar 18, 2013 |
| Contact name |
Tao Cai |
| E-mail(s) |
caitao@nibs.ac.cn
|
| Organization name |
National Institute Of Biological Sciences, Beijing (NIBS)
|
| Lab |
Sequencing Facility
|
| Street address |
No. 7 Science Park Road, Zhongguancun Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE39637 |
Gene expression in pluripotent and TSKM-iPS induction cells. |
| GSE39639 |
Gene expression and 5hmC/5mC state in pluripotent and TSKM-iPS induction cells |
|
