|
| Status |
Public on Apr 25, 2012 |
| Title |
HD MSN 60Q clone2 |
| Sample type |
RNA |
| |
|
| Source name |
HD MSN
|
| Organism |
Homo sapiens |
| Characteristics |
cag length: 60
disease state: HD
cell type: iPS-derived MSN-like
|
| Treatment protocol |
n/a
|
| Growth protocol |
Differentiated human iPS-derived NSCs, with additional 56d differentiation to striatal-like cells. NSC lines were generated by collagenase treating (1mg/ml, Gibco) iPSC colonies and lifting them from the feeder layers directly into Stemline medium (Sigma) supplemented 100ng/ml basic FGF (Chemicon), 100ng/ml EGF (Chemicon), and 5?g/ml heparin (Sigma) in polyhema-coated flasks to prevent attachment. iPSC-derived NSCs were expanded as spherical aggregates and passaged weekly with a chopping technique. To generate striatal-like cells, growth medium containing EGF/FGF was removed from NSCs, and cells were plated on laminin or allowed to aggregate for 5 days in NIM (1% N2 in DMEM:F12). BDNF (20ng/ml; Peprotech 450-02) was then added for 2 days. The medium was then supplemented for 21 days with BDNF, rhShh (200ng/ml; R&D 1845-SH), and Dkk1 (100ng/ml; R&D 1096-DK-010). The rest of the differentiation was then completed in NIM with BDNF, dibutyryl cyclic AMP (dbcAMP, 0.5mM; Sigma D0260) and valproic acid (VPA, 0.5mM; Sigma P4546). Medium was half-changed twice per week or as needed. If cells were differentiated as aggregates, they were plated on day 42.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were identified as HD or control by genotyping. Samples were snap frozen in liquid N2. RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment.
|
| Label |
biotin
|
| Label protocol |
Standard 100ng total RNA labeling protocol (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
Sample name: MSN60i.3
|
| Data processing |
Partek Genomics Suite Version 6.6 Beta (6.12.0207) was used for data processing. Only interrogating probes were imported. No probe filtering was done. RMA background correction was done. Quantile Normalization was applied. Log Probes using Base 2. Probeset summarization Median Polish was done.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
|
| |
|
| Submission date |
Apr 23, 2012 |
| Last update date |
Apr 25, 2012 |
| Contact name |
Leslie Thompson |
| E-mail(s) |
lmthomps@uci.edu
|
| Organization name |
University of California, Irvine
|
| Street address |
Biological Sciences III
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL10739 |
| Series (1) |
| GSE37517 |
Expression data from human induced pluripotent stem cell derived NSCs and striatal-like cells |
|
