|
| Status |
Public on May 06, 2015 |
| Title |
ESC_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E3.5 derived ESCs
passages: 20-25
strain: OCT4-deltaPE-GFP x C57BL/6
|
| Growth protocol |
ESCs were grown on MEFs in N2B27 media supplimented with 2I (CHIR99021, 3uM; PD0325901, 1uM) and LIF(Millipore) 10ug/ml; EpiSCs were grown on MEFs in N2B27 media containing 12ng/ml FGF2 and 20ng/ml Activin-A supllementated with 20% KSR; IS-EPIs were grown on MEFs in N2B27 media containing 20ng/ml and IWR1 2.5uM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of all samples was extracted using Rneasy Mini Kit (Qiagen) and subjected to amplification with MessageAmpII aRNA kit (Ambion) per manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
The Affymetrix GeneChip microarrays was performed by the Functional Genomics Core Facility at The Salk Institute for Biological Studies following the manufacturer’s protocol (Affymetrix, Santa Clara, CA). Briefly, 100 ng of total RNA of each sample were processed using Affymetrix GeneChip 3’ IVT Expression Kit following the manufacturer’s protocol. For each sample, 12.5 μg fragmented and labeled aRNA were hybridized to the Affymetrix PrimeView Human Gene Expression Arrays.
|
| |
|
| Hybridization protocol |
After hybridization cocktails preparation, the Affymetrix GeneChip Primeview Gene Expression Arrays were hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.
|
| Scan protocol |
Expression signals were scanned on an Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
E3.5 derived ESCs
|
| Data processing |
CEL files were analyzed using the oligo package in R/Bioconductor and normalized using RMA
|
| |
|
| Submission date |
Aug 19, 2014 |
| Last update date |
May 07, 2015 |
| Contact name |
Christopher Benner |
| E-mail(s) |
cbenner@ucsd.edu
|
| Organization name |
University of California, San Diego (UCSD)
|
| Department |
Medicine
|
| Street address |
9500 Gilman Dr. MC 0640
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0640 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (2) |
| GSE60523 |
An alternative pluripotent state confers interspecies chimaeric competency [Microarray] |
| GSE60605 |
An alternative pluripotent state confers interspecies chimaeric competency |
|
