Agencourt rna clean magnetic beads

RNA tissue (10–20 mg) for each brain sample included in the sequencing study was homogenized in TRIzol (Invitrogen, Carlsbad, CA). Total RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen Sciences Inc., Germantown, MD) and further purified using Agencourt RNA Clean magnetic beads (Beckman Coulter, Inc.). The quantity and purity of the RNA was determined by absorbance at 260 nm and by 260/280 absorbance ratio, respectively. Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and the RNA integrity number (RIN) was measured on an Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit (Agilent, Foster City, CA).

Raw sequencing reads of post-mortem prefrontal cortex (BA9) samples from 29 individuals with PD and 44 neurologically healthy individuals were analyzed [11 (link)]. All control and PD brain samples were derived from males of European ancestry without significant Alzheimer’s disease pathology. The average age of death for the PD group was 77.55 and 70 years for the control group. Original data are freely available from the Sequence Read Archive (SRA) (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA283498, accessed on 7 November 2020). For RNA extraction, brain samples were homogenized in TRIzol (Invitrogen, Carlsbad, CA, USA), then total RNA fraction was isolated using the Qiagen RNeasy Mini Kit (Qiagen Sciences Inc., Germantown, MD, USA) and purified using Agencourt RNA clean magnetic beads (Beckman Coulter, Inc., Carlsbad, CA, USA). RNA-Seq library preparations were made using Illumina’s TruSeq RNA Sample Prep Kit according to the manufacturer’s protocol. Samples were sequenced using 2 × 100 nt paired-end runs on Illumina’s HiSeq 2000 system [11 (link)].