GSE198212

Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO

1. Processed Using https://github.com/YeoLab/eclip 0.7.0
2. After standard HiSeq demultiplexing, eCLIP libraries with distinct in-line barcodes were demultiplexed using custom scripts, and the random-mer was appended to the read name for later usage.
3. Reads were then adapter trimmed (cutadapt v1.9.dev1) and reads less than 18 bp were discarded
4. Mapping was then first performed against human elements in RepBase (v18.05) with STAR (v2.4.0i), repeat-mapping reads were segregated for separate analysis, and all others were then mapped against the full human genome (hg19) including a database of splice junctions with STAR (v 2.4.0i) (Dobin et al., 2013).
5. Uniquely mapping reads were then run through a custom-built PCR duplicate removal script, removing duplicate reads based on sharing identical Read1 start position, Read2 start position, and random-mer sequence to leave 'Usable' reads.
6. eCLIP data sets with multiple in-line barcodes were merged at the usable read stage, and cluster identification was performed on usable reads using CLIPper (Yeo et al., 2009) (available at https://github.com/YeoLab/clipper/releases/tag/1.0) with options –s GRCh38 –o –bonferroni –superlocal–threshold-method binomial–save-pickle
7. data are further downsampled to roughly equal number per replicate

Supplementary Files (7)

Linked Publications (2)