Project description:<p>Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples (n = 7) from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed, and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue (<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0093993">Chan et al., 2014</a>).</p> <p>Data from the primary progressive multiple sclerosis (PPMS) brain specimens (n = 14) and Normal Control brain specimens (n = 14) are also submitted here. All the subjects studied here (encephalitis, PPMS, and controls) were selected from existing collections at the Rocky Mountain and UCLA brain banks. These selections were performed by the directors at the two centers (Dr. Corboy at RM and Nagra at UCLA) based on clinic information provided at the time of collection. All the specimens are from deidentified deceased individuals. The submitting investigators have no identifying information on any of these subjects. To avoid confusion, the dbGaP Subject IDs are identical to the brain bank identifying numbers.</p>
Project description:We analyzed the transcriptome profile of B cells from patients with relapsing-remitting multiple sclerosis (RRMS), patients with primary progressive multiple sclerosis (PPMS) and healthy individuals. High-density Clariom D Arrays for human were used to quantify the transcript levels. This GEO entry provides the processed Clariom D microarray data from the gene-level and exon-level workflows.
Project description:The transcriptome of normal-appearing white matter for relapse-remitting multiple sclerosis (MS), primary progressive MS and secondary progressive MS was determined using total RNA-sequencing. We then performed a differential gene analysis comparing the normal-appearing white matter for each clinical subtype of MS with non-MS control tissue
