NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1303145 Query DataSets for GSM1303145
Status Public on Mar 16, 2014
Title 25 years old Female_2
Sample type RNA
 
Source name 25 years old Female_2
Organism Homo sapiens
Characteristics age: 25 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 25 years old Female_2
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 8.301614261
1053_at 4.882862143
117_at 5.091347226
121_at 7.418917136
1255_g_at 4.896297859
1294_at 5.488425895
1316_at 5.449795938
1320_at 4.350288958
1405_i_at 3.610903994
1431_at 4.684218191
1438_at 5.846101075
1487_at 6.056788931
1494_f_at 5.444478068
1552256_a_at 6.398859819
1552257_a_at 7.042141879
1552258_at 4.319983096
1552261_at 5.15053635
1552263_at 3.440015054
1552264_a_at 7.141127958
1552266_at 4.051922295

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1303145_25BF.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