Protocols

Assay pipeline

• Protocols:RNA_extraction
• Protocols:HeliScopeCAGE
• Protocols:Low_quantity_HeliScopeCAGE
• Protocols:nanoCAGEscan
• Protocols:SmallRNAseq
• Protocols:RNAseq

Computational Pipeline

• Protocols:rRNAdust
• Protocols:HeliScopeCAGE_read_alignment - delve, filtering (Q20 + percent identity), CTSS
• Protocols:RNAseq_read_alignment - TopHat, Cufflinks, (Trinity), Cuffmerge
• Protocols:SmallRNAseq_read_alignment - BWA

Computational analysis

• Protocols:CAGE_peak_calling

The Gene Ontology enrichment analysis for the following data sets

• Protocols:GOstat_on_coexpression_cluster
• Protocols:GOstat_on_MARA_motif_target

was performed using GOstat (PMID:14962934) on gene lists with all known genes (human or mouse) as background. term significant at FDR 5% (Benjamin-Hochberg) were retained.

• Protocols:Sample_enrichment_analysis_on_CAGE_peak_expression
• Protocols:Sample_enrichment_analysis_on_coexpression_cluster
• Protocols:Motif_Activity_Response_Analysis(MARA)