|
| Status |
Public on Feb 09, 2013 |
| Title |
Neuron, Hmgn1-/-, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Neuron, Hmgn1-/-
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/B6
tissue: Neuron
genotype: Hmgn1-/-
|
| Growth protocol |
The ES cells were co-cultured with mitomycin-c treated mouse primary embryonic fibroblast feeders or cultured under feeder-free conditions, they were maintained in Knock-out Dulbecco’s modified Eagle’s medium, with 20% serum replacement, 0.055 mM β-mercaptoethanol, 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5000 U/ml penicillin/streptomycin, and 1000 U/ml LIF. In vitro differentiation of ES cells along neural lineage was performed using the Mouse Dopaminergic Neuron Differentiation Kit (R&D System) according to the manufacturer’s instruction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by RNeasy Mini Kit (Qiagen) followed by “on-column” DNase I treatment according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
Scanning was performed with the Affymetrix GeneChip scanner using default settings.
|
| Description |
Gene expression data from Neuron
|
| Data processing |
All analysis was performed using R and BioConductor. Expression levels were derived using the Robust Multichip Average (RMA) protocol with default setting and differentially expressed genes were identified using an empirical Bayes method implemented in the R package “Limma”
|
| |
|
| Submission date |
Feb 08, 2013 |
| Last update date |
Feb 09, 2013 |
| Contact name |
Iris Zhu |
| E-mail(s) |
iris.zhu@nih.gov
|
| Organization name |
National Institute of Health
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20894 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE44175 |
Expression data from mouse embyonic stem cell, neural progenitor and neuron |
|
