|
| Status |
Public on Aug 31, 2013 |
| Title |
Wildtype H9 hESC derived NSC 1 |
| Sample type |
RNA |
| |
|
| Source name |
Human NSC
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: WT / WT
|
| Treatment protocol |
H9 cells were collected at passage 38. H9-NSCs were collected at passage 2. H9-CMs were collected on day25 of differentiation.
|
| Growth protocol |
H9 cells were cultured in mTeSR. H9-NSCs were cultured in NSC maintainance medium. H9-CMs were cultured in RPMI/B27 medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Qiagen).
|
| 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 |
Gene expression data
|
| Data processing |
The statistical analysis of the data was performed using GenePattern platform from Broad Institute. Briefly, raw CEL files were imported into GenePattern platform and normalized using RMA algorithm. The Hierarchical Clustering analysis was performed using the HierarchicalClustering module of the software. The dendrograms and the heat map of the clustered gene expression data were visualized by the HierarchicalClusteringViewer module.
|
| |
|
| Submission date |
Jun 24, 2013 |
| Last update date |
Aug 31, 2013 |
| Contact name |
Fei Yi |
| E-mail(s) |
feiyi34@gmail.com
|
| Organization name |
Salk Institute
|
| Lab |
GEL-B
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE48257 |
Gene expression analysis of H9 hESC derived cardiomyocytes (CM) and neuron stem cells (NSC) |
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