eCLIP-seq and knockdown RNA-seq datasets of RNA-binding proteins

We retrieved paired eCLIP-seq and KD-RNA-seq (knockdown followed by RNA sequencing) datasets from the Encyclopedia of DNA Elements project (ENCODE, https://www.encodeproject.org/)³¹, covering 85 and 107 different RBPs in HepG2 and K562 cell lines, respectively. All raw sequencing reads were first subjected to Trimmomatic (version 0.39)⁶⁸ to remove adapters and low-quality bases. For eCLIP-seq data, we followed the ENCODE processing pipeline³¹ to obtain enriched binding regions for each RBP. Trimmed KD-RNA-seq reads were mapped to the human reference genome (GRCh38) by using STAR (version 2.7.6a) in two-pass mode⁵². The alignments were then subjected to StringTie (version 2.1.4)⁵³ with our assembled transcriptome to quantify transcript abundance. Finally, DESeq2 (version 1.30.0)⁶⁹ was applied to compare transcript differences between RBP-knockdown and control cell lines for each RBP.