miR-eCLIP +siRNA
Data Analysis
•Locate off targets transcriptome-wide
•Effects of siRNA modifications on targeting
•Map endogenous microRNA:mRNA binding
Example: Identify Number of siRNA Off Targets
Robust identification of siRNA off targets is crucial when performing RNAi. This bar plot shows the number of siRNA off target peaks (red) detected in each sample, as well as off target peaks that are reproducible across replicates. In addition to identifying siRNA targets, miR-eCLIP +siRNA also provides unbiased information on where endogenous miRNAs are binding. The number of per-sample and reproducible peaks from endogenous miRNAs are shown in teal.
All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.
Interactive Summary Data Analysis Report: miR-eCLIP +siRNA
Bioinformatics
Our Comprehensive Data Analysis Package
Eclipsebio’s standard analysis uses human (hg38). Contact us for alternate species including viral genomes.
RAW SEQUENCING DATA | FASTQ
Reads directly off sequencer and demultiplexed per sample for data back-up and publication
GENOME ALIGNMENTS | BAM
Unique AGO2 eCLIP sequence alignments to the genome. Reads aligned to repetitive elements were filtered out and PCR duplicates were removed.
COVERAGE TRACKS | BIGWIG
Normalized read coverage on positive and negative strands for visualization in a genome viewer such as IGV
AGO2, miRNA, & siRNA PEAKS | BED
Table listing the binding locations and relative enrichment of siRNAs and miRNAs
TARGET SUMMARY REPORT | HTML
HTML report containing plots, enriched GO terms and KEGG pathways, HOMER motif analysis, and repetitive element mapping information for enriched peaks.
