Ebbert_lab_PBMC_long_read_single_cell_PIPseq_project
ALL DATA HERE ARE DE-IDENTIFIED. Dataset from PBMCs isolated from 43-year-old healthy Caucasian male in two replicates (PBMC1 and PBMC2). PBMCs were isolated using an optimized version of the Sepmate protocol (V2.0.0; Stemcell Technologies, #85450). cDNA preparation for each sample was performed using a modified long-read PIPseq protocol (detailed in the Doyle et al preprint) and sequenced using three Oxford Nanopore Promethion R10 flow cells. The modified PIPseq protocol used the T20 V4.0PLUS Single Cell RNA Kit, developed by Fluent Biosciences, and targeted 30,000 cells per sample. For the ONT portion of the protocol, the SQK-PCS114 kit was used. Sequencing yielded a mean raw 245.9 million reads per sample, which translated to 100.95 million reads per sample after filtering for reads with a corrected barcode and a mapping quality (MAPQ) >10. This repository contains sequencing output directories compressed into .tar.gz files, containing basecalled FASTQ files for passed and failed reads. More information can be obtained from the original preprint written from this data and the GitHub repositories associated with the articles.Preprint: https://www.biorxiv.org/content/10.1101/2025.10.16.682832v1GitHub for preprocessing pipeline: https://github.com/UK-SBCoA-EbbertLab/single_cell_nextflow_pipeline.GitHub for analyses: https://github.com/UK-SBCoA-EbbertLab/single_cell_analysis_PBMCs/tree/main.Reference files, annotations, and outputs from long-read scRNA-seq pipelines and ColabFold protein modeling are publicly available at Zenodo: (http://doi.org/10.5281/zenodo.17341210).