Dataset related to the article "Design of novel multiplex MinION sequencing workflow based on the required depth required to analyse human primary cell cDNA"

This record contains raw data related to the article “Design of novel multiplex MinION sequencing workflow based on the required depth required to analyse human primary cell cDNA" Abstract Background Transcript sequencing is a crucial tool for gaining a deep understanding of biological processes in diagnostic and clinical medicine. Given their potential to analyse novel complex eukaryotic transcriptomes, long-read sequencing technologies are able to overcome some limitations of short-read RNA-sequencing approaches. Oxford Nanopore Technologies (ONT) offers the ability to generate long-read sequencing data via portable protein nanopore USB devices at a reasonable cost. The aim of this study was to identify the depth needed to achieve the best trade-off between accuracy and cost-effectiveness by multiplex ONT MinION sequencing of human cell RNA. Results We analysed four cDNA libraries from isolated human aortic valve interstitial cells, by an ONT MinION sequencer. Synthetic datasets with different sizes were generated to evaluate the performance as a function of the read number. We were able to detect a high number of genes (>12,500) with ~2 million reads, whose expression measurements were comparable to the full dataset (rp = 0.98). These data were further confirmed by the implementation of a new and user-friendly multiplexing method, including of 6 custom designed barcodes integrated in the reverse transcription step. We obtained comparable results between the different barcoded samples, both in terms of the number of identified genes (average value >12,500) and expression levels (rp>0.86). Conclusions ONT sequencing allows a batch of six different barcoded samples to be efficiently analysed in a unique MinION run. Thus, these data support the use of our sequencing workflow for human cells to further decrease run time and cost per sampleThis work was supported by the Italian Ministry of Health funds (Ricerca Finalizzata: GR-2018-12366423; ERA-CVD: PICASSO-JTC-2018-042) and by Fondazione Gigi e Pupa Ferrari ONLUS (FPF-14)