|Public on Jun 21, 2021
|midbrain dopamine neurons
|case number (refer to table in paper): 17
disease status: Control
|Lysis buffer is directly added to the cells after laser capture. No RNA extraction is conducted. The cell lysate is direcly used for library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.
|Illumina HiSeq 2000
|Base-calling using Illumina Cassava 1.7
Alignment to the human genome (hg38) performed using STAR with default parameters. RPKM were estimated using ¨rpkmforgenes¨ (Ramsköld et al., 2009).
For cases having more than 1 replicate per group, corresponding samples were averaged before the analysis so that each Case have only 1 SNc and 1 VTA.
Differential gene expression analysis was performed on the read counts using DESeq version 1.16.1. Only genes with reads in at least one third of the samples or more were considered in the analysis.
Supplementary_files_format_and_content: One processed data file is added providing abundance measurements (RPKM) organized as a matrix for all samples (tab-delimited txt).
|May 25, 2018
|Last update date
|Jun 21, 2021
|Department of Biochemistry and Biophysics
|Svante Arrhenius v. 16C
|RNAseq of human SNc and VTA midbrain dopamine neurons isolated from post mortem material of control subjects and Parkinson's Disease patients using laser capture microdisection.