Comment[ArrayExpressAccession] E-GEOD-40710 MAGE-TAB Version 1.1 Public Release Date 2012-10-04 Investigation Title aSyn polyA-RNAseq in PD and unaffected cortical brain samples Comment[Submitted Name] aSyn polyA-RNAseq in PD and unaffected cortical brain samples Experiment Description We sought to more precisely characterize the different alpha-synuclein (aSyn) 3M-bM-^@M-^YUTR mRNA species in normal and PD human brain. High-throughput, whole-transcriptome sequencing of the 3M-bM-^@M-^YUTR ends of polyadenylated mRNA transcripts (termed pA-RNAseq; see Methods) was performed on a cohort of 17 unaffected and 17 PD cerebral cortical tissue samples. This revealed 5 aSyn 3M-bM-^@M-^YUTR isoforms, with lengths of 290, 480, 560, 1070 and 2520 nt. Of these, the 560 nt and 2520 nt forms were predominant. The existence and relative preponderance of these species was further confirmed by Northern Blot. We next hypothesized, that aSyn 3M-bM-^@M-^YUTR selection might be altered in PD. Comparison of pA-RNAseq profiles from PD and unaffected cerebral cortex samples revealed an increase in the preponderance of the long 3M-bM-^@M-^YUTR species (>560 nt) relative to shorter species (<560 nt). Such a relative increase in aSynL was confirmed by Quantitative real-time RT-PCR (rt-qPCR) and appeared specific for PD, as the increase was also observed by comparison to RNA from amyotrophic lateral sclerosis patient samples. We note that the modified aSyn 3M-bM-^@M-^YUTR selection associated with PD patient tissue was detected in cerebral cortex tissue, which typically harbors pathological evidence of the disease process without frank cell loss; thus, this phenotype is unlikely to be a secondary consequence of neurodegeneration. Comparison of 3'UTR ends of alpha-synuclein in PD and unaffected brain cortex Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name RHINN Abeliovich Rhinn Person First Name Herve Asa Herve Person Email hr2239@columbia.edu Person Affiliation Columbia University Person Phone 2123051150 Person Fax 2123051150 Person Address Columbia University, 650 W. 168th. St., New York, New York, USA Person Roles submitter Protocol Name P-GSE40710-4 P-GSE40710-1 P-GSE40710-3 P-GSE40710-2 Protocol Description Illumina reads were converted to FASTQ Sanger format using FASTQ Groomer (Galaxy) The first 27 bp at their 5M-bM-^@M-^Yends of the reads were trimmed using FASTQ Trimmer to remove the polyA and adapters sequences The reads were mapped to human hg19 genome using Burrows-Wheeler Alignment tools with GalaxyM-bM-^@M-^Ys default settings allowing 4% of missing alignments. Genome_build: hg19 Supplementary_files_format_and_content: Processed files contain the quantification for each sample of the 5 3'UTR isoforms detected for alpha-synuclein None RNA was extracted from frozen brain tissue using miRNeasy kits (Qiagen) and quantified using a Nanodrop (Thermo). First-strand cDNA was synthesized from 1 M-NM-