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Sample GSM701370 Query DataSets for GSM701370
Status Public on Sep 15, 2011
Title Wild-type neurons day 22, rep1
Sample type RNA
 
Source name NAS2 neurons day 22
Organism Homo sapiens
Characteristics cell type: Neurons
genotype: wild-type
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 Wild-type neurons day 22
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

Data table header descriptions
ID_REF
VALUE Quantile normalized gene level expression values from Partek Genomics Suite v6.5

Data table
ID_REF VALUE
3881686 9.66125
3332247 3.15164
2867102 2.93605
3076899 3.31577
2672712 8.61833
2342980 3.14238
2842570 10.1011
3526544 6.03392
2317557 3.3097
2902531 4.50317
3746362 5.24926
2402942 7.03419
3382216 7.61493
3771800 8.29064
3746365 3.24072
2427469 6.89956
2392945 4.7238
3991617 6.66649
2453006 3.90354
2537379 3.22281

Total number of rows: 27053

Table truncated, full table size 419 Kbytes.




Supplementary file Size Download File type/resource
GSM701370.CEL.gz 21.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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