subject id: 941 age: 88 Sex: male race: white postmortem interval minutes: 245 ph: 6.2 clinical dementia rating: 0.5 braak neurofibrillary tangle score: 6 neuropathological category: Possible AD average neuritic plaque density: 5.52 sum of cerad rating scores in multiple brain regions: 9 sum of neurofibrillary tangles density in multiple brain regions: 8 brain region: Putamen tissue: post-mortem brain
Treatment protocol
N/A
Growth protocol
N/A
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated from 50 mg tissue aliquots from brain tissue samples, amplified to cRNA, and biotin-labeled for analysis on the Affymetrix U133AB or U133 Plus 2.0 Human genome GeneChip at Gene Logic Inc. (Gaithersburg, MD, USA) using the TRIzol method and RNeasy columns according to protocols from Affymetrix (Santa Clara, CA, USA). The 28S/18S rRNA ratio of isolated RNA was assessed using a Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) Label – biotin label protocol => followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).
Label
biotin
Label protocol
followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).
Hybridization protocol
followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).
Scan protocol
followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).
Data processing
The raw microarray data was preprocessed using the robust multiarray Average (RMA) method function implemented in the R/Bioconductor package Affy (v1.44) using the default parameters, including quantile normalizion and log2 transformation. RMA normalization was performed separately for each brain region. For 17 brain regions profiled with both 133A and 133B arrays, 133A and 133B arrays were normalized separately and combined afterwards. Finally, the normalized gene expression data was corrected for covariates including sex, PMI (postmortem interval), pH and race using linear regression.
