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Service Report

IMMAGINA Biotechnology S.r.l.

06/11/2024

Thank you for choosing IMMAGINA Biotechnology for your Nano-tRNAseq experiments! This report provides a comprehensive overview of your results, with easy-to-read graphs and charts that bring your data to life.

If you have any questions about the experiment, please don’t hesitate to contact us at



1. Samples description

2. Alignment Statistics

Percentage of reads aligned to tRNAs. A non-redundant set of tRNAs that differ in at least 10% of their sequence was used to reduce multi-mapping artefacts, thus information about isodecoders may have been lost. Only uniquely mapped reads were considered for further analysis.

4. Interactive Scatterplot Visualizing tRNA Abundances for Individual Samples

Scatterplot of nuclear-encoded tRNAs

Scatter plots of tRNA abundances by aminoacid type across samples.

Scatterplot of mitochondrial-encoded tRNAs

Scatter plots of tRNA abundances by aminoacid type across samples.

5. Interactive Heatmap Visualizing Putative tRNA Modifications in Individual Samples

Heatmap of nuclear-encoded tRNAs

Heatmap of the difference in summed basecalling errors between two samples.

6. Interactive Principal Component Analysis for Treated vs. Control Comparisons

7. Interactive Scatterplot Comparing normalized tRNA Abundances Between Treated and Control Groups

8. Interactive Volcano Plot Highlighting Differential tRNA abundances Between Treated and Control Groups

9. Interactive Heatmap Displaying Log2 Fold Change (log2FC) and Adjusted p-values at the Single-Nucleotide Level from Differential tRNA Modifications Analysis Between Treated and Control Groups

10. Interactive Filtered Heatmap Displaying Significant tRNA Modifications (Adjusted p-values < 0.05) at the Single-Nucleotide Level Between Treated and Control Groups

11. Outputs

* pod5 sequencing files
* Demultiplexed alignment BAM files
* Table with n° of uniquely mapped reads for each tRNA (counts.tsv). It can be used to reproduce the scatterplots.
* Table with n° of times a nucleotide was basecalled correctly or an error (mismatch,insertion or deletion) was made for each tRNA nucleotide in each sample (heatmap.base_count.tsv). Only quality-filtered, uniquely mapped reads were considered for the analysis of basecalling errors. The first 25 nt of each tRNA correspond to the 5’ adapter. The last 30 nt of each tRNA correspond to the 3’ adapter.
* Table with the sum of basecalling errors (mismatches and deletions) for each tRNA nucleotide divided by the depth of coverage for that position in each sample (heatmap.base_freq.tsv). It can be used to reproduce the heatmaps. Only quality-filtered uniquely mapped reads were considered for the analysis of basecalling errors. The first 25 nt of each tRNA correspond to the 5’ adapter. The last 30 nt of each tRNA correspond to the 3’ adapter.

12. Data visualization guidelines

It is possible to visualize single tRNA tracks on IGV. Simply:
1. Download the latest version of IGV
2. Start IGV
3. Select the provided tRNA database as reference genome
4. Load the BAM files. Note that these files contain all the aligned reads, independently of their quality or if they map uniquely or not

13. Contents of Results folder