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Sample GSM208649 Query DataSets for GSM208649
Status Public on Jan 01, 2008
Title Medial substantia nigra control case 4 - A chip
Sample type RNA
 
Source name Post-mortem medial substantia nigra
Organism Homo sapiens
Characteristics age: 77; gender: F
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol (http://www.qiagen.com). Tissue samples were mechanically disrupted using a rotary homogenizer, lysed in buffer containing guanidine isothiocyanate (GITC) and then further homogenized (Shredder tubes, Qiagen).
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to a Human Genome 133 A array (HG_U133A; Affymetrix). The GeneChips was washed and stained in an Affymetrix Fluidics Station 400. Standard Affymetrix Protocols were used (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).
Scan protocol Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).
Description Gene expression data from medial substantia nigra (MNCON4A)
Data processing CEL files were read using ArrayAssist software (version 4.1, Stratagene) and PathwayStudio 5 (Ariadne). Intensity values were derived applying the (GeneChip) Robust Multi Array (RMA) algorithm.
 
Submission date Jul 09, 2007
Last update date Aug 14, 2011
Contact name Linda B Moran
Organization name Imperial College London
Department Neuropathology
Street address Fulham Palace Road
City London
ZIP/Postal code W6 8RF
Country United Kingdom
 
Platform ID GPL96
Series (1)
GSE8397 Expression profiling of the Parkinsonian Brain

Data table header descriptions
ID_REF probe set name
VALUE RMA-calculated Signal intensity

Data table
ID_REF VALUE
1007_s_at 10.14601119
1053_at 4.588619898
117_at 3.676460201
121_at 7.381588133
1255_g_at 2.497802042
1294_at 5.720824421
1316_at 3.946245294
1320_at 2.813201138
1405_i_at 5.736357421
1431_at 3.225261886
1438_at 2.304196201
1487_at 6.414548232
1494_f_at 4.796391347
1598_g_at 7.780948546
160020_at 4.425118005
1729_at 4.412593012
177_at 3.475332271
1773_at 3.029529651
179_at 5.925184469
1861_at 4.587432198

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM208649.cel.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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