This interactive report provides an overview of eRibo Pro results, accessible at the different tabs. For each table and plot, the button can be clicked to get more information. The menus in the top right corner of each plot can be used to modify the plots (zoom, hide samples, and save a copy of the plot). This report is optimized for viewing on a desktop and plots have been tested on several browsers but in some cases they may not render correctly, please use an alternate browser if plots do not load.

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Experiment Summary

This report summarizes an eRibo Pro experiment where HEK293 cells were treated with either Torin, a translation inhibitor, or a DMSO control. Full methods details are available upon request. The following samples are included in the analysis:

Sample group RPF RNA-Seq
Treated RPF_Torin_Rep1, RPF_Torin_Rep2 RNASeq_Torin_Rep1, RNASeq_Torin_Rep2
Untreated RPF_Untreated_Rep1, RPF_Untreated_Rep2 RNASeq_Untreated_Rep1, RNASeq_Untreated_Rep2

This tab summarizes quality control metrics for the RNA-Seq and ribosome protected footprint (RPF) libraries.

Quality Control Metrics

The following table shows important quality control metrics for each sample. Two libraries are made for each sample, one containing ribosome protected footprints (RPFs) and one from the whole transcriptome (RNA-Seq). For each sample ("Sample"), two rows are included that list the metrics for each library. The identity of the library is included in the "Library" column. The following columns describe the processing of the libraries:

  1.  Initial reads: the number of sequenced reads for each library.
  2.  % Pass trim: reads first underwent adapter trimming to remove both adapters and sequences shorter than 18 nucleotides. The percentage of sequenced reads that passed this trimming step is listed in this column.
  3.  % Repetitive elements: trimmed reads are aligned to Eclipsebio's custom database of repetitive elements. This database includes rRNAs, tRNAs, snoRNAs, and other features. The percentage of trimmed reads that were filtered is listed in the column.
  4.  % Uniquely aligned to the genome: the remaining reads from the repetitive element filtering were aligned to the genome, and the percent of those reads that map uniquely to the genome is listed in this column.
  5.  % PCR duplicates: PCR duplicates were defined as uniquely mapped reads that map to the same read coordinates and have an identical unique molecular identifier (UMI). The percentage of mapped reads that were identified as PCR duplicates is included in this column.
  6.  Final reads: this column lists the number of uniquely mapped, deduplicated reads that were used for this analysis.
Sample Library Initial reads % Pass trim % Repetitive elements % Uniquely aligned to the genome % PCR duplicates Final reads

Gene Coverage Range

Pairs of ribosome protected footprint (RPF) and RNA-Seq libraries were prepared from each sample. The plot below shows the distribution of RPM (reads per million) normalized gene counts in each of the libraries.