Code and processed data for: RNA-binding protein depletion reveals reproducible, protein-specific differences between lncRNA and mRNA responses

Code and processed data for the manuscript: Szcześniak MW, Wanowska E. RNA-binding protein depletion reveals reproducible, protein-specific differences between lncRNA and mRNA responses (submitted for publication, 2026). The study re-analyses 860 ENCODE RNA-seq experiments in which one of 473 RNA-binding proteins was depleted by shRNA knockdown or CRISPR knockout in K562 or HepG2 cells, and compares each lncRNA with mRNAs matched for expression, gene length, splicing efficiency and stability. Files: lncrna-rbp-depletion_code_v1.0.zip, the analysis and figure scripts (also at https://github.com/michal-szczesniak/lncrna-rbp-depletion; MIT License); lncrna-rbp-depletion_data_v1.0.tar.gz, processed data: per-experiment DESeq2 results, log2 fold-change matrices and their standard errors, class effects of all experiments, results of the other analyses, the data behind each figure panel, derived gene annotation tables and ENCODE metadata (figure images are not included; the scripts draw them from these tables); README_data.md, the layout of the data archive. Raw data are available from the ENCODE portal; accession numbers are listed in data/meta.