RNA-seq libraries were prepared with ScriptSeq v2 (Illumina), QuantSeq (Lexogen), or SMARTer Pico v2 (Takara) kits. Splicing isoform quantification was performed using MISO and rMATS packages. The bind-n-Seq experiment was performed as previously described (45 (link)), with minor modifications. Targeted DMS-MaPseq was performed as previously described (33 (link)), with minor modifications. SNRPA1 irCLIP-seq was performed as described (39 (link)), with minor modifications.
Protocol detail
Quantification of Splicing Isoforms and RNA-Binding Events
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Corresponding Organization : UCSF Helen Diller Family Comprehensive Cancer Center
Other organizations : University of Pennsylvania, McGill Genome Centre, McGill University, Queen Mary University of London, Rockefeller University, Yale University, Yale Cancer Center
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Variable analysis
independent variables
- RNA-seq library preparation method (ScriptSeq v2, QuantSeq, or SMARTer Pico v2)
- Splice isoform quantification method (MISO and rMATS packages)
- Bind-n-Seq experiment with minor modifications
- Targeted DMS-MaPseq with minor modifications
- SNRPA1 irCLIP-seq with minor modifications
- Splicing isoform quantification
- Bind-n-Seq binding profiles
- Targeted DMS-MaPseq probing of RNA structure
- SNRPA1 binding regions identified by irCLIP-seq
- None explicitly mentioned
- None explicitly mentioned
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