age: 65 Sex: female post mortem interval (hr): 3.5 apoe genotype: E3/E4 ba_rin: 6.9 ba8s18s: 0.804 disease state: HD (grade IV)
Extracted molecule
total RNA
Extraction protocol
Post-mortem tissue samples from healthy controls (Ctrl) of mean age 60 y/mean PMI 22 h; and from patients with advanced AD Braak & Braak stage III-VI (80 y/17 h), FTD (72 y/NA) and HuD (71 y/19 h), were snap frozen in liquid N2 and stored at -80°C in the Brown University Brain Tissue for Neurodegenerative Disorders Resource Center until processed. RNA from CP was extracted using TRIzol reagent in accordance with instructions by manufacturer (Thermo-Fisher, Grand Island, NY). Isolated RNA samples were assayed for quality via the Agilent RNA 6000 Pico Kit on Agilent Bioanalyzer (Santa Clara, CA) and RNA yield via Quanti-iT RiboGreen RNA Assay Kit (Thermo-Fisher).
Label
biotin
Label protocol
Samples were amplified and labeled using an automated version of the NuGEN Ovation WB protocol after normalizing to 50 ng total RNA input (NuGEN Technologies, San Carlos, CA).
Hybridization protocol
Hybridization (45°C for 18 h), labeling, and scanning, using Affymetrix ovens, fluidics stations, and scanners, were conducted following the protocols recommended (NuGEN Technologies). Gene expression profiling was performed with a customized Human Affymetrix GeneChip microarray (GEO platform GPL 10379) that included 57,060 probesets (Affymetrix, Santa Clara, CA).
Scan protocol
Hybridization (45°C for 18 h), labeling, and scanning, using Affymetrix ovens, fluidics stations, and scanners, were conducted following the protocols recommended (NuGEN Technologies). Gene expression profiling was performed with a customized Human Affymetrix GeneChip microarray (GEO platform GPL 10379) that included 57,060 probesets (Affymetrix, Santa Clara, CA).
Data processing
Data were normalized by robust multiarray average (RMA).
Comparative Transcriptomics of Choroid Plexus in Alzheimer's Disease, Huntington's Disease and Frontotemporal Dementia: Implications for CSF Homeostasis and Dynamics
