{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Maha Alfaidi"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16863"],"description":["The dataset consists of single-cell RNA sequencing (scRNA-seq) profiles of fetal human cortical neurons (10 weeks gestation) under six experimental conditions: Sample 1 – Control: Untreated cells. Sample 2 – PFF treated: Cells exposed to alpha-synuclein pre-formed fibrils (PFF) for 14 days. Sample 3 – PFF + B36D: Cells treated with PFF and the peptide inhibitor B36D. Sample 4 – B36D alone: Cells treated with B36D without PFF. Sample 5 – PFF + S62: Cells treated with PFF and the peptide inhibitor S62. Sample 6 – S62 alone: Cells treated with S62 only. Culture and treatment timeline: All cells were initially cultured for 7 days before treatment. Treatments were applied for 14 days. On day 21 in vitro, cells were dissociated for single-cell RNA sequencing. This dataset captures the gene expression changes associated with PFF-induced pathology and the potential rescue effects of peptide inhibitors B36D and S62 in human cortical neurons. It allows comparisons between control, disease-mimicking, and treatment conditions at single-cell resolution."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Single-cell RNA-seq libraries were prepared using a droplet-based platform (10x Genomics Chromium) following the manufacturer’s protocol. Briefly, single cells were encapsulated with barcoded beads, and reverse transcription was performed to generate cDNA. Amplified cDNA was used for library construction, including fragmentation, end repair, adapter ligation, and PCR amplification.","Sample Collection - Human fetal cortical neurons were cultured under standard conditions and treated with alpha-synuclein preformed fibrils (PFFs) and/or peptide inhibitors as indicated. At defined time points, cells were collected and dissociated into single-cell suspensions using TrypLE (Thermo Fisher Scientific, 12605010) according to the manufacturer’s instructions. Cells were washed and resuspended for downstream single-cell library preparation.","Sequencing - Libraries were sequenced on an Illumina platform NovaSeq 6000 using paired-end sequencing with a read length of 150 bp. Sequencing was performed according to the manufacturer’s instructions to generate high-quality transcriptomic data.","Nucleic Acid Extraction - RNA extraction was not performed separately. Instead, single-cell suspensions were directly processed for single-cell RNA-seq library preparation, where cell lysis and RNA capture were performed within the workflow according to the manufacturer’s protocol."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw sequencing reads were quality-checked using FastQC and trimmed where necessary. Reads were aligned to the human reference genome (GRCh38) using STAR aligner. Gene-level counts were generated using featureCounts. Normalization and differential gene expression analysis were performed using DESeq2 in R. Count data were normalized using the median of ratios method, and differential expression was calculated using a negative binomial model. Adjusted p-values were obtained using the Benjamini–Hochberg method."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Parkinson's disease (PD) is a prevalent, chronic neurodegenerative disorder characterised by the progressive loss of dopaminergic neurons in the substantia nigra and other brain regions. The aggregation of alpha-synuclein (α-syn) into Lewy bodies and neurites is a key pathological feature associated with PD and its progression. Many therapeutic studies aim to target these aggregated forms of α-syn to potentially slow down or stop disease progression in PD. This review provides a comprehensive analysis of recent clinical trials involving vaccines and monoclonal antibodies targeting α-syn. Specifically, UB-312, AFFITOPE PD01A, PD03A and ACI-7104.056 are designed to provoke an immune response against α-syn (active immunisation), while Prasinezumab and Cinpanemab, MEDI1341 and Lu AF82422 focus on directly targeting α-syn aggregates (passive immunisation). Despite some promising results, challenges such as variable efficacy and trial discontinuations persist. Future research must address these challenges to advance disease-modifying therapies for PD around this therapeutic target."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["An update on immune-based alpha-synuclein trials in Parkinson’s disease","Early α-synuclein–mediated mitochondrial dysfunction in a human cell model of Parkinson’s disease dementia"],"pubmed_authors":["Maha Alfaidi; Roger A. Barker; Wei-Li Kuan","Maha S. Alfaidi, Léa M. D. Wenger, Kornélia Szebényi, Thomas B. Stoker, Xiaoling He, Shaline V. Fazal, Jana Sebestikova, Amir Jassim, Richard J. Gilbertson, Raquel Garza, Johan Jakobsson, Maria Grazia Spillantini, Roger A. Barker, and Wei-Li Kuan","Maha Alfaidi"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA sequencing (scRNA-seq) profiles of fetal human cortical neurons","description":"The dataset consists of single-cell RNA sequencing (scRNA-seq) profiles of fetal human cortical neurons (10 weeks gestation) under six experimental conditions: Sample 1 – Control: Untreated cells. Sample 2 – PFF treated: Cells exposed to alpha-synuclein pre-formed fibrils (PFF) for 14 days. Sample 3 – PFF + B36D: Cells treated with PFF and the peptide inhibitor B36D. Sample 4 – B36D alone: Cells treated with B36D without PFF. Sample 5 – PFF + S62: Cells treated with PFF and the peptide inhibitor S62. Sample 6 – S62 alone: Cells treated with S62 only. Culture and treatment timeline: All cells were initially cultured for 7 days before treatment. Treatments were applied for 14 days. On day 21 in vitro, cells were dissociated for single-cell RNA sequencing. This dataset captures the gene expression changes associated with PFF-induced pathology and the potential rescue effects of peptide inhibitors B36D and S62 in human cortical neurons. It allows comparisons between control, disease-mimicking, and treatment conditions at single-cell resolution.","dates":{"release":"2026-04-09T00:00:00Z","modification":"2026-04-09T15:59:28.25Z","creation":"2026-04-07T11:44:16.44Z"},"accession":"E-MTAB-16863","cross_references":{"ENA":["ERP191813"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1007/s00415-024-12770-x"]}}