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Sample GSM1303158 Query DataSets for GSM1303158
Status Public on Mar 16, 2014
Title 44 years old Female
Sample type RNA
 
Source name 44 years old Female
Organism Homo sapiens
Characteristics age: 44 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 44 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 8.115228878
1053_at 5.17719612
117_at 5.055831664
121_at 7.340902803
1255_g_at 4.548907223
1294_at 5.603109128
1316_at 5.627191071
1320_at 4.577108396
1405_i_at 3.310959557
1431_at 4.69331153
1438_at 5.521188051
1487_at 6.43879438
1494_f_at 5.24024662
1552256_a_at 6.528865356
1552257_a_at 7.381473978
1552258_at 4.493824264
1552261_at 5.149932741
1552263_at 3.215937736
1552264_a_at 7.259643967
1552266_at 4.05960618

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1303158_44F.CEL.gz 7.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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