Dynamic characterization and interpretation for protein–RNA interactions across diverse cellular conditions using HDRNet

We collected 261 RNA binding site datasets from https://www.nature.com/articles/s41422-021-00476-y for 172 RBPs constructed using the same flag-marked technique in K562, HepG2, HEK293, HEK293T, HeLa and H9 cell lines from the ENCODE project and POSTAR. Of these datasets, there are 65 CLLP-seq datasets for 61 RBPs from POSTAR and 196 eCLIP datasets for 111 RBPs from the ENCODE project. In terms of the RBP binding data in tissues, the processed MBNL2 (Muscleblind Like Splicing Regulator 2) binding peak data in human brain tissues (GSE68890) were curated from POSTAR; the DGCR8 and HNRNPU binding data in human adrenal gland were collected from ENCODE; and the MBNL1 (Muscleblind Like Splicing Regulator 1) binding data in brain, heart, muscle, and myoblasts from mice were obtained from (GSE39911). These datasets were quality controlled and processed using a uniform pipeline to ensure consistent results.