Comprehensive Analysis of RNA-Protein Interactions by High Throughput Sequencing-RNA Affinity Profiling

These data were generated using a method that we call High Throughput Sequencing- RNA Affinity Profiling (HiTS-RAP) that transcribes DNA at each cluster on an Illumina flowcell, and then use it to measure the affinity of mutants of two RNA aptamers at an unprecedented scale. We measured dissociation constants for 1,875 mutants of the GFP aptamer (GFPapt), and 9,832 mutants of NELFapt, an RNA aptamer that binds Drosophila NELF-E (Negative Elongation Factor E), an RNA binding subunit of a protein complex involved in maintaining promoter proximally paused RNA Polymerase II. We analyzed these data to determine sequence and structural features of these two aptamers that are most important for their protein interactions. These files contain the raw sequence information from this study. GFPapt data come from three lanes of a GAIIx, and NELF from a single lane. Our custom files contain coordinates on the flowcell, sequence, quality score, average fluorescence intensity during sequencing, and then fluorescence intensities from protein binding steps.