NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1303153 Query DataSets for GSM1303153
Status Public on Mar 16, 2014
Title 34 years old Female
Sample type RNA
 
Source name 34 years old Female
Organism Homo sapiens
Characteristics age: 34 years old
Sex: Female
Growth protocol The postmortem brain tissue samples were neuropathologically normal for age, and were derived from non-demented individuals. Tissue was procured in accordance with institutional guidelines. Human cortical grey matter samples were dissected from the frontal pole (Brodmann area 9, 10), and were snap frozen in liquid nitrogen and stored at -85ºC. Human brain samples with a tissue pH > 6.5 were used to exclude prolonged terminal hypoxia
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Dissected cortical grey mater was cut into small pieces in the frozen states and ~70 mg was homogenized immediately in Trizol (Gibco) and RNA was isolated. RNA that was intact by electrophoresis and had an A260/A280 ratio ≥ 1.9 was used for cDNA synthesis. cDNA synthesis, cRNA synthesis and fragmentation, and preparation of the hybridization cocktail were carried out according to the Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual)
 
Hybridization protocol Hybridizations were performed in the Genechip hybridization over 640 (60vrpm) for 16 hrs at 45ºC. The probe arrays were then washed, stained in the GeneChip Fluidics Station 400 operated by GeneChip software following the appropriate fluidics protocols.
Scan protocol Affymetrix Microarray Suite 5.0 was utilized to generate Affymetrix present/absent calls. Probe-level Liner Model (PLM) was used to normalize the arrays at probe level and compute model-based expression values using the PM only model. The dChip software www.dchip.org, [3] was used for clustering visualization.
Description 34 years old Female
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Jan 08, 2014
Last update date Jun 26, 2019
Contact name Tun-Hsiang Yang
E-mail(s) yangth@gmail.com
Organization name HMS
Department Genetics
Lab Yankner
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL570
Series (1)
GSE53890 REST and Stress Resistance in Aging and Alzheimer’s Disease
Relations
Reanalyzed by GSE133349

Data table header descriptions
ID_REF
VALUE log2-MAS5.0 signal intensity

Data table
ID_REF VALUE
1007_s_at 8.879737619
1053_at 5.113059377
117_at 6.205210495
121_at 7.265236552
1255_g_at 4.903444411
1294_at 5.463652355
1316_at 5.411621482
1320_at 4.490916504
1405_i_at 3.505287571
1431_at 4.697605839
1438_at 5.449312407
1487_at 6.276385115
1494_f_at 5.28522767
1552256_a_at 6.559678553
1552257_a_at 7.208147229
1552258_at 4.382770115
1552261_at 5.089087751
1552263_at 3.161361751
1552264_a_at 6.85451664
1552266_at 4.039638596

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1303153_34F.CEL.gz 7.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap