DISREGARD. Deep bulk RNAseq of neurological controls and PD brains

erroneous sub-version. This Zenodo deposit contains a publicly available description of the Dataset: Title: "Deep bulk RNAseq of neurological controls and PD brains". Description: Human post-mortem brain tissue from donors with Lewy Body pathology and neurologically healthy controls was sourced from the Cambridge Brain Bank under London–Bloomsbury Research Ethics Committee (REC reference no. 16/LO/0508). Donors with Lewy Body pathology (n=25) had a clinical diagnosis of Parkinson's disease and were compared to an age- and sex-matched group of neurologically healthy control donors (n=18) who had no history of neurological illness. A neuropathologist assessed all cases for Lewy Body pathology Braak staging, co-existing proteinopathies and other pathologies. Fresh frozen tissue was sampled from SN, PUT, AMY, and PFC at the level of Brodmann area 46 (PFC). A 3 mm3 tissue piece was cut from the same tissue block that had been used for snRNA sequencing and disrupted using a Tissuelyser (Qiagen). A steel bead and RLT buffer with -mercaptoethanol was added to the Tissuelyser and shaken at 30 Hz for 2 minutes. Total RNA was isolated from the disrupted tissue using the RNeasy Mini Kit (Qiagen; RRID). The sequencing libraries were then generated using Illumina TruSeq Stranded mRNA library prep kit (with poly-A selection) and sequenced on a NovaSeq6000 or Novaseq X plus (2 x 150 paired end). Basecalling and sample-specific fastq files were done using Illumina's bcl2fastq in default parameters. Reads were uniquely mapped to hg38 reference genome using STAR aligner (version 2.7.8a; REF; RFID, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.03). TE and gene quantification was performed using featureCounts (subread package version 1.6.3; REF; RFID -s 2) and gencode annotation version 38, repeatmasker (open-4.0.5, filtered from tRNAs, simple repeats, small RNAs, and low-complexity regions), or retrotector predictions annotation. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset