ebbert_lab_brain_long_read_cDNA_discovery_project

ALL DATA PRESENT HERE ARE DE-INDENTIFIED. THESE DATA ARE ALSO AVAILABLE THROUGH SYNAPSE: https://www.synapse.org/#!Synapse:syn52047893/wiki/622953. Synapse also contains the ".txt" files with the "sequencing_summary" information outputted by Guppy basecaller. #### DATA DESCRIPTION #### Dataset with 12 postmortem aged brain samples from Brodmann area 9/46 (dorsolateral frontal cortex). We had samples from 6 Alzheimer's disease (AD) cases and 6 controls. From the 6 AD cases, 3 were male and 3 female. From the 6 controls 3 were male and 3 female. Each sample was sequenced using one full Oxford Nanopore PromethION flow cell. We used kit SQK-PCS11 (PCR amplified cDNA sequencing). Sequencing yielded an average of 35.5 million aligned reads per sample after filtering out all reads with a mapping quality <10.This repository contains all the raw ".fastq" sequencing files. All these data are compressed using gzip and can be found under "Files". Metadata from the samples can be found in the "sample_metadata.tsv" file under "Files". #### MORE INFO #### More information can be obtained in the original article published with these data and/or from the GitHub associated with the article. GitHub: https://github.com/UK-SBCoA-EbbertLab/brain_cDNA_discovery Article (pre-print): https://www.biorxiv.org/content/10.1101/2023.08.06.552162v2 Processed data (counts matrices, extended annotations, etc...) and annotations used to analyze this data in the original publication can be accessed through Zenodo: Zenodo: https://doi.org/10.5281/zenodo.8180677 Data from this repository analyzed in the original article can be easily queried and visualized through in this web interface:https://ebbertlab.com/brain_rna_isoform_seq.html