Project description:The impact of gDNA contamination on RNA-seq experiments performed with the prime-seq method was assessed by introducting artifical contamination using mouse gDNA this enables us to identify contamination by species specific assignment of mapped reads.
Project description:Analysis of cerebrospinal fluid (CSF) is important for diagnosis of neurological diseases. Specific proteins, which are released from the CNS can be quantitatively monitored. Especially, in the field of neurodegenerative diseases abnormal protein abundance is an important biomarker. However, the quality of the CSF sample is a key factor for the analytic outcome. In this study we evaluated the effect of blood contamination in CSF with respect to protein biomarker identification. We compared three distinct measures: semiquantitative Combur10-Test® strips for urinary hemoglobin, a specific hemoglobin ELISA and bottom-up mass spectrometry (MS) based proteomics for the determination of the general blood contamination level. In parallel, we studied the impact of blood contamination on the detectability of alpha-synuclein (aSyn), a highly abundant protein in blood/erythrocytes and potential biomarker for Parkinson’s disease. Based on our results we identified other markers for blood contamination beyond hemoglobin and defined a grading system for blood levels in CSF samples including a lower limit of tolerable blood contamination for mass spectrometry-based biomarker studies and suggest the Combur10-Test® as a cost-effective test for simple and fast determination of blood contaminations in CSF.
