Data files

Sample preparation for proteomics analysis was performed as described previously with slight modifications. Briefly, for mouse samples, SDC lysis buffer (2% SDC, 100 mM Tris-HCl pH 8.5) was used to lyse the cell pellets at 95°C for 45 min at 600 rpm in a thermoshaker. For human samples which were fixed in PFA, prior to the SDC lysis buffer step, the samples were first resuspended in 6% SDS buffer, heat denatured, sonicated and then precipitated using 80% acetone overnight in -20°C. Next day, these ...

After respective treatment, cells were washed 2 times with ice-cold DPBS, scraped in PBS and pellets either processed immediately or stored at -80°C. Cells were lysed in RIPA buffer for 30 min on ice. After clearance by centrifugation at 20,000 × g for 10 min at 4 °C, protein concentrations were adjusted using BCA assay. Cleared and adjusted supernatants were incubated overnight on an overhead rotator with preequilibrated streptavidin agarose (Sigma). Next day, beads were washed 2 times with RIPA ...

Tryptic in solution digestion of the purified myelin fraction was performed according to the filter-aided sample preparation (FASP) protocol (Erwig et al., 2019) originally described by Manza et al., 2005; followed by LC-MS-analysis. In brief, purified myelin fractions corresponding to 10 µg myelin protein were dissolved and lysed in lysis buffer (1% ASB-14, 7 M urea, 2 M thiourea. 10 mM DTT 0.1 M Tris pH 8.5). Homogenised samples were diluted with lysis buffer containing 2% CHAPS to reduce ASB-14 ...

The dataset contains FASTQ files referring to the study "Small RNA sequencing from CSF extracellular vesicles - PD/CTR". For this project, RNA was isolated from CSF extracellular vesicles obtained by ultracentrifugation. Libraries were prepared with the TruSeq Small RNA library prep Illumina, and sequencing conducted in the Illumina HiSeq4000.

Cerebrospinal fluid samples of patients with Parkinson’s disease and healthy controls were used in this study. After tryptic digestion, all samples were spiked with indexed retention time (iRT) peptides and were measured using a DIA mass spectrometry approach. The CSF samples were prepared for digestion using consecutively RapiGestTM SF Surfactant, DTT and iodoacetamide. Then, proteolytic digestion was performedby trypsin solution and stopped by TFA. Dried peptides were resuspended in TFA. The ...

The dataset contains FASTQ files referring to the study "Multi-omics analysis of Parkinson’s disease midbrains". For this project, RNA was isolated from human postmortem midbrain tissue (PD and Control samples). Libraries were prepared with the TruSeq Small RNA library prep (Small RNA Seq) and the TruSeq Stranded Total RNA Kit (for transcriptomics), both from Illumina. Sequencing for both experimental setups was conducted in the Illumina HiSeq4000.

We generated AAV(L):bPGRN (L = liver, b = brain-penetrant), a liver-targeting adenovirus (AAV) encoding a fusion protein (8D3:PGRN) consisting of a single chain fragment variable (scFv) antibody recognizing mouse TfR (transferrin receptor) fused to human PGRN (hPGRN). To study the effects of AAV(L):bPGRN, we treated 6-week old wildtype or GRN,TMEM106B double knock-out mice with either 1.3 x 10^13 vg/kg AAV or isotonic saline solution (0.9% NaCl) intravenously via tail vain injection. 9-10 weeks ...