E-AFMX-6 - Transcription profiling of caudate nucleus, frontal cortex, and cerebellum samples from 44 Huntingtons disease HD-gene-positive cases and 36 age and sex-matched controls
Released on 8 February 2006, last updated on 1 May 2014
Affymetrix GeneChip microarray analyses of caudate nucleus, frontal cortex, and cerebellum samples were conducted with RNA extracted from fresh-frozen samples collected with minimal postmortem interval to autopsy from 44 HD-gene-positive cases and 36 age- and sex-matched controls (Supplemental Table A). All samples were carefully selected based on RNA quality and antemortem variables, and the HD cases were additionally analyzed based on the presence or absence of disease symptoms and Vonsattel grade of disease pathology (scale=0-4; Vonsattel et al.,1985). Tissues were collected from precise anatomical regions and stored at -80 deg. C. Where available for each case, frozen blocks of the head of the caudate nucleus, frontal cortex (primary motor cortex [Brodmann's Area 4] or superior frontal cortex [Brodmann's Area 9]) and cerebellum (non-vermal cerebellar hemisphere) were further dissected to provide 200 mg tissue samples for RNA extraction. Pathological grading of HD cases was performed from corresponding formalin-fixed, paraffin-embedded caudate nucleus sections according to the Vonsattel scale (Vonsattel et al., 1985), by two neuropathologists with special interest and expertise in HD pathology. This grading scale is based on the overall pattern of neuropathology of the caudate nucleus and on the numbers and ratio of neurons and astrocytes. A subset of cases were cross-referenced across collection sites to confirm consistency of the grading procedure. DNA was extracted from all cases and controls and genotyped for the CAG repeat length alleles in IT15 (HD gene), as described previously (Warner et al., 1993). Post-mortem interval to autopsy was available for the majority of samples and detailed clinical information for many. RNA integrity was assessed by capillary electrophoresis on a bioanalyzer 2100 (Agilent) using 300ng of total RNA. RNA quality was assigned on a 4 point scale. Most samples rated poor were not processed further.
transcription profiling by array, co-expression, disease state, organism part comparison
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