ena-STUDY-UNIVERSITY OF TORONTO-08-09-2021-18:33:03:613-1614
HTR-SELEX rawdata for experiments performed with 23 RNA binding proteins for the study: "PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA binding proteins"
Study describes a new bioinformatics approach for modelling specificities of RNA binding proteins that takes into account both the sequence and structural features of the RNA. High throughput RNA Systematic Evolution of Ligands Through Exponential Enrichment (HTR-SELEX) method was modified from approach described in Jolma et al. 2020. "Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences" (PMID: 32703884). In this study we performed new HTR-SELEX experiments for 23 RNA binding proteins and their raw fastq data is deposited in this entry. Information about the experiments is encoded both in metadata and in the originally submitted sample file names. In the sample names the information is separate by underscore "_" symbols. For example sample named "HNRNPC_AT40NCCTTGG_AAN_D_Cycle1.fastq.gz" Means that it is derived for experiment using: 1) Protein HNRNPC, 2) selection ligand where the randomised region is flanked by AT and CCTTGG residues (when it is in the dsDNA state), 3) It is from experimental batch "AAN", 4) Experimental 96-well plate "D" and 5) From the first selection cycle of the assay.
Study describes a new bioinformatics approach for modelling specificities of RNA binding proteins that takes into account both the sequence and structural features of the RNA. High throughput RNA Systematic Evolution of Ligands Through Exponential Enrichment (HTR-SELEX) method was modified from approach described in Jolma et al. 2020. "Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences" (PMID: 32703884). In this study we performed new HTR-SELEX experiments for 23 RNA binding proteins and their raw fastq data is deposited in this entry. Information about the experiments is encoded both in metadata and in the originally submitted sample file names. In the sample names the information is separate by underscore "_" symbols. For example sample named "HNRNPC_AT40NCCTTGG_AAN_D_Cycle1.fastq.gz" Means that it is derived for experiment using: 1) Protein HNRNPC, 2) selection ligand where the randomised region is flanked by AT and CCTTGG residues (when it is in the dsDNA state), 3) It is from experimental batch "AAN", 4) Experimental 96-well plate "D" and 5) From the first selection cycle of the assay.