|
| Status |
Public on Jun 14, 2014 |
| Title |
Control-iPSC-derived NSC 2 |
| Sample type |
RNA |
| |
|
| Source name |
Control-iPSC-derived NSC 2
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: FANCA(+/+)
cell type: iPSC
disease state: control
|
| Treatment protocol |
The induced NSC were cultured at passage 2
|
| Growth protocol |
Cells were cultured in NSC maintainance 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 microarray 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, 10ug fragmented and labeled aRNA (final concentration of the aRNA on the array is 0.05ug/ul) were hybridized to the Affymetrix PrimeView chips
|
| |
|
| Hybridization protocol |
After hybridization cocktails preparation, the Affymetrix PrimeView 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 from wildtype fibroblasts
|
| 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 |
Sep 13, 2012 |
| Last update date |
Jun 14, 2014 |
| 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) |
| GSE40865 |
Global gene expression analysis for neuron stem cells (NSC) derived from iPSCs with Fanconi Anemia |
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