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Sample GSM763977 Query DataSets for GSM763977
Status Public on Sep 15, 2011
Title Wild-type iPSCs, NAS9
Sample type RNA
 
Source name Wild-type iPSCs
Organism Homo sapiens
Characteristics cell line: NAS9
cell type: induced pluripotent stem cells (iPSCs)
genotype/variation: wild-type
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

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

Data table
ID_REF VALUE
1007_s_at 8.82135
1053_at 9.40182
117_at 4.01753
121_at 5.52373
1255_g_at 6.08418
1294_at 4.26579
1316_at 5.75827
1320_at 4.2855
1405_i_at 4.28715
1431_at 3.70789
1438_at 4.61967
1487_at 6.3318
1494_f_at 4.01124
1552256_a_at 7.15597
1552257_a_at 8.42809
1552258_at 3.4338
1552261_at 4.01345
1552263_at 6.87401
1552264_a_at 7.28445
1552266_at 3.65962

Total number of rows: 54613

Table truncated, full table size 996 Kbytes.




Supplementary file Size Download File type/resource
GSM763977_A653_ver_2_1504.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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