|
| Status |
Public on Sep 15, 2011 |
| Title |
SNCA triplication iPSCs, AST13 |
| Sample type |
RNA |
| |
|
| Source name |
SNCA triplication iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AST13
cell type: induced pluripotent stem cells (iPSCs)
genotype/variation: SNCA triplication
|
| Treatment protocol |
not applicable
|
| Growth protocol |
iPSCs: grown in mTESR1 media on BD Matrigel;
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus kit (Qiagen). cDNA synthesis and amplification was performed using the Ambion®WT Expression Kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
total RNA
|
| Data processing |
Data were processed using Partek Genomics Suite v6.5. Arrays were preprocessed together with publicly available array data (GSE16190, GSE19902, GSE22499, GSE26451, GSE7179, GSE7879, GSE8590 and GSE9440) using RMA quantile normalization with GC background correction.
|
| |
|
| Submission date |
Jul 19, 2011 |
| Last update date |
Sep 15, 2011 |
| Contact name |
Tilo Kunath |
| E-mail(s) |
tilo.kunath@ed.ac.uk
|
| Phone |
+44 (0) 131 651 9500
|
| Organization name |
University of Edinburgh
|
| Department |
Centre for Regenerative Medicine
|
| Street address |
5 LIttle France Drive
|
| City |
Edinburgh |
| ZIP/Postal code |
EH16 4UU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE30792 |
Expression data from Parkinson's iPSCs with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative |
|
