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Sample GSM920931 Query DataSets for GSM920931
Status Public on Apr 25, 2012
Title control MSN 28Q
Sample type RNA
Source name control MSN
Organism Homo sapiens
Characteristics cag length: 28
disease state: control
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: MSN4.2
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
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

Data table header descriptions
VALUE RMA signal estimates from Partek Genomics Suite Version 6.6 Beta (6.12.0207)

Data table
7892501 3.95278
7892502 5.1613
7892503 3.8929
7892504 9.32397
7892505 3.45307
7892506 4.30059
7892507 6.59804
7892508 7.93223
7892509 11.0237
7892510 4.10605
7892511 4.72491
7892512 8.15453
7892513 4.35405
7892514 11.296
7892515 9.83253
7892516 2.50918
7892517 7.82447
7892518 3.45015
7892519 6.00267
7892520 9.80106

Total number of rows: 257430

Table truncated, full table size 3994 Kbytes.

Supplementary file Size Download File type/resource
GSM920931_1111F-02_15-MSN56d-4.2_HuGene-1_0-st-v1_.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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