Sample: 36 Diagnosis: SCZD Age (Years): 59 Race: Caucasian Death Cause: Embolism Treatment: Haloperidol Post Mortem Interval: 13 hours Brain pH: 6.67 RIN1: 8.4
Extracted molecule
polyA RNA
Extraction protocol
Sample preparation: was as previously described (Paz et al., 2006; Bullock et al., In Press). Cerebellar samples were from 14 patients with a diagnosis of SCZ according to DSM-IV criteria and six controls. Samples were obtained from the Maryland Brain Collection with the permission of the Maryland Brain Collection Steering Committee. Permission for the study of brain tissue was provided by families in accordance with the guidelines of the Uniform Anatomical Gift Act. Approval for the study was obtained from the Institutional Review Board of the University of Maryland. Cortical areas corresponding to crus I/VIIa of cerebellar hemispheres were dissected at -20 ºC and frozen at -80 ºC, as described (Bullock et al., In Press). The average pH of the samples was 6.6 + 0.17. Cerebellum specimens were obtained according to NIH guidelines for confidentially and privacy. Genomic DNA and total RNA were isolated from samples using standard techniques (Qiagen, Valencia, CA).
Label
not applicable
Label protocol
not applicable
Hybridization protocol
not applicable
Scan protocol
not applicable
Description
na
Data processing
Read Alignment-based gene expression profiling: Reads were aligned to the human genome and RefSeq transcript databases (Pruitt et al., 2005) using the algorithm GMAP (Wu and Watanabe, 2005) and the software system Alpheus (Sugarbaker et al., 2008), with adjustments for short SBS reads (oligomer overlap interval = 3nt, identities > 34/36 or 94%). Only the highest scoring alignment(s) was retained. Reads with a single best alignment or with equally good alignments to alternative transcripts of the same gene were considered uniquely aligned. Aligned read frequencies (per million aligned reads) were calculated for each sample and gene using Alpheus (Sugarbaker et al., 2008). read frequencies were log10 transformed prior to evaluation of inter-sample differences.
