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Sample GSM545732 Query DataSets for GSM545732
Status Public on Dec 31, 2011
Title C016_Control_M_60
Sample type RNA
 
Source name Brain BA22 post-mortem control
Organism Homo sapiens
Characteristics gender: Male
age: 60
post-mortem delay: 16h
ph: 6.9
disease state: control
tissue: superior temporal cortex (Brodmann Area 22, BA22)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen BA22 using a Polytron type homogenizer (YellowLine DI 25 Basic) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1 ml of TriZol to 20 mg of tissue. RNA was further purified using RNeasy mini-columns (Qiagen, Valencia, CA, USA) including on-column DNAse-1 step and elution in water. Although pH was analysed in brain lysates using a pH meter, this was not considered to be rigorous enough to exclude or include samples and instead the RNA integrity number (RIN) was used to assess the quality of the RNA as the primary inclusion criterion. The quantity of extracted RNA was determined by spectrophotometry and quality was assessed using an Agilent 2100 Bioanalyzer (South Plainfield, NJ, USA) to determine the RIN. Based on the RIN, samples were classified into three quality groups—pass (RIN >7.0); borderline (RIN 6.0–7.0); fail (RIN<6.0). Following classification, there were 41 pass (RIN range of samples 7.0–9.0: average=7.7), 16 borderline (RIN range of samples 6.0–6.9; average=6.4) and 5 fail samples. Samples in the fail category were excluded from the study, and the remaining samples were randomized into four batches, containing an equal number of schizophrenic/control and male/female samples, for target generation and hybridization.
Label biotin
Label protocol For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).
 
Hybridization protocol For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).
Scan protocol Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip Operating Software (Affymetrix).
Description n/a
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 150.
 
Submission date May 20, 2010
Last update date Dec 31, 2011
Contact name Julie Huxley-Jones
E-mail(s) julie.x.huxley-jones@gsk.com
Phone 01438 768416
Organization name GlaxoSmithKline Pharmaceuticals
Department Computational Biology
Street address Gunnels Wood Road
City Stevenage
State/province Hertfordshire
ZIP/Postal code SG1 2NY
Country United Kingdom
 
Platform ID GPL570
Series (1)
GSE21935 Comparison of post-mortem tissue from Brodman Brain BA22 region between schizophrenic and control patients

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 203.0833893
AFFX-BioB-M_at 282.4426575
AFFX-BioB-3_at 157.7346191
AFFX-BioC-5_at 440.4044189
AFFX-BioC-3_at 435.2972717
AFFX-BioDn-5_at 761.9511108
AFFX-BioDn-3_at 2489.916992
AFFX-CreX-5_at 5311.812988
AFFX-CreX-3_at 6338.169922
AFFX-DapX-5_at 19.32037926
AFFX-DapX-M_at 7.217090607
AFFX-DapX-3_at -8.294836044
AFFX-LysX-5_at 11.58279133
AFFX-LysX-M_at -9.487931252
AFFX-LysX-3_at 12.82285118
AFFX-PheX-5_at -3.070569515
AFFX-PheX-M_at -7.13383913
AFFX-PheX-3_at 21.99476433
AFFX-ThrX-5_at 1.625823736
AFFX-ThrX-M_at -4.182668686

Total number of rows: 54675

Table truncated, full table size 1223 Kbytes.




Supplementary file Size Download File type/resource
GSM545732_jrs_U133p2_DB2_6_C016_R97500.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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