Ebbert Lab Nanopore PCS111 brain cDNA discovery (12 samples - AD vs Controls)

For more information about this data see the publication: https://doi.org/10.1038/s41587-024-02245-9

The publication GitHub is a good source of information: https://github.com/UK-SBCoA-EbbertLab/brain_cDNA_discovery

There are also README files in the data that provide more information about what is contained in each directory.

Basic information about main directory structure and files:

reproducing_RNA_figures - Contains all references/annotations necessary for reproducing the stats, analysis, and figures for the RNA isoform analysis in the article.

reproducing_nextflow_pipeline - Contains all references/annotations necessary for reproducing the NextFlow pipeline.

proteomics - Fasta reference files files used for proteomics analysis with FragPipe and results output by FragPipe.

transcriptomic_analysis_output - Contains output from transcriptomic analysis including: quality control, counts matrices, new RNA isoform annotations, and the Bambu R object.

counts_transcript.txt - Transcript level counts (does not include any intronic reads).