|
| Status |
Public on Sep 15, 2011 |
| Title |
SNCA triplication fibroblasts |
| Sample type |
RNA |
| |
|
| Source name |
AST fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblasts
genotype: SNCA triplication
|
| Growth protocol |
Fibroblasts: grown in DMEM/FCS, brought to equivalent passage; iPSCs: grown in mTESR1 media on BD Matrigel; Neurons: differentiated according to the dual SMAD/ floor plate protocol, then enriched for dopaminergic neurons.
|
| 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 |
SNCA triplication fibroblasts
|
| Data processing |
Data were processed using Partek Genomics Suite v6.5. Arrays were preprocessed using RMA quantile normalization with GC background correction. Gene level summary signals were generated by calculating the median expression value of all probe sets annotated to a transcript.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na30.hg19.probeset_core.mps
|
| |
|
| Submission date |
Apr 04, 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 |
GPL5175 |
| Series (2) |
| GSE28365 |
Expression data from fibroblasts, iPSCs and neurons with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative |
| GSE28367 |
Expression and SNP data from fibroblasts, iPSCs and neurons with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative |
|
