LRB-IIMCB/ninetails_processing: v1.0.0

Scripts, supplementary data and additional info used in the developing of the Ninetails R package. 

Data and resources stored in this record are supplement to the research paper entitled "Direct profiling of non-adenosines in poly(A) tails of endogenous 
and therapeutic mRNAs with Ninetails".

The copy of GitHub repository containing source code of Ninetails R package is available here: https://zenodo.org/records/13309819

Table of content:

• LRB-IIMCB/ninetails_processing-v1.0.0.zip - a copy of Github repository, contains docker container with Ninetails (ready to use), scripts used for training datasets preparation & neural network training
• Supplementary_Data_1.xlsx - Sample metadata, hardware & software specs, CNN architecture & performance (benchmark)
• Supplementary_Data_2.xlsx - Summarized data used for orthogonal validation of Ninetails/Nanopore vs FLAMseq/PacBio based on datasets from publicly available repositories (Legnini et al. 2019 [https://www.nature.com/articles/s41592-019-0503-y] and Tavakoli et al. 2023 [https://www.nature.com/articles/s41467-023-35858-w]).
• Supplementary_Data_3.xlsx - Summarized data used for comparison of non-adenosine incorporation frequency by various enzymes based on an in vitro synthesized molecules analyzed with Ninetails pipeline.
• Supplementary_Data_4.xlsx - Summarized data from moderna mRNA-1273-derived reads obtained as a result of crude mRNA-1273 and bone-marrow derived murine macrophages subjected to mRNA-1273 in various time points analyzed with Ninetails pipeline. Reads were classified based on pentamer (UCUAG) presence/absence with DTW algorithm described by Krawczyk et al. 2023 [https://www.biorxiv.org/content/10.1101/2022.12.01.518149v2].
• Supplementary_Data_5.xlsx - Summarized data from reads corresponding to murine endogenous transcripts bone-marrow derived murine macrophages subjected to mRNA-1273 in various time points analyzed with Ninetails pipeline.
• Supplementary_Data_6.xlsx - Summarized data from reads corresponding to murine endogenous transcripts from various cell types (bone-marrow derived murine macrophages, dendritic cells, B cells, T cells) analyzed with Ninetails pipeline.
• ninetails_raw_analysis_outputs.zip - output files produced by Ninetails and FLAMseq pipelines. The Ninetails produces 2 types of outputs per analyzed sample: read classification (general info, whether read contains non-adenosines in poly(A) or not) and residue classification (which type of non-adenosine is present in given poly(A) tail). The FLAMseq used for orthogonal validation produces single file, corresponding with general classification. In this archive, files were merged according to the source/organism/protocol. The samples were named according to the identifiers/aliases provided in Supplementary_Data)1.xlsx
• Supplementary_Information.pdf - additional figures, notes and references supplementing the original work.