High-Throughput Studies of HuR-Associated RNAs in Human Endothelial Cells Using Ultrasensitive Small RNA Sequencing (raw data and scripts)

This dataset contains bioinformatic scripts, curated reference sequences and raw sequencing datasets used for the preparation of the manuscript entitled "High-Throughput Studies of HuR-Associated RNAs in Human Endothelial Cells Using Ultrasensitive Small RNA Sequencing" by Turchinovich et al, 2026. The file Turchinovich_et_al_scripts_NAR.txt provides step-by-step command-line instructions used for processing sequencing data and reproducing analyses corresponding to figures in the manuscript. The scripts are designed to run in Shell/Bash environments with downstream analysis performed in R using Bioconductor packages. The dataset includes manually curated reference sequences packaged in RefSeqs.zip, which were used for sequence alignment during data processing. These references are required for the execution of the SEQIRA analysis pipeline. Raw sequencing data are provided as FASTQ files and are organized into directories corresponding to the figures presented in the manuscript to facilitate reproducibility. Each directory contains the raw reads and the scripts used for their processing. Figures 2-3. Crosslinked RIP-seq HuRSCRI_S10.fastq.gz - anti-HuR RIP-seq replicate 1 IgGSCRI_S9.fastq.gz - control IgG RIP-seq replicate 1 HuRSCRII_S14.fastq.gz - anti-HuR RIP-seq replicate 2 IgGSCRII_S13.fastq.gz - control IgG RIP-seq replicate 2 Figure 4. DiCLIP-seq BAHuR_S1.fastq.gz - CATL anti-HuR DiCLIP-seq BAIgG_S2.fastq.gz - CATL control IgG DiCLIP-seq CAHuR_S5.fastq.gz - CATS anti-HuR DiCLIP-seq CAIgG_S6.fastq.gz - CATS control IgG DiCLIP-seq Figure 5. Validation of DiCLIP-seq on more replicates from lower inputs AHuRR1_S9.fastq.gz - anti-HuR rep 1 IgGR1_S10.fastq.gz - control IgG rep 1 AHuRR2_S15.fastq.gz - anti-HuR rep 2 IgGR2_S16.fastq.gz - control IgG rep 2 AHuRR3_S1.fastq.gz - anti-HuR rep 3 IgGR3_S2.fastq.gz - control IgG rep 3 AHuRR4_S5.fastq.gz - anti-HuR rep 4 IgGR4_S6.fastq.gz - control IgG rep 4 AHuRR5_S7.fastq.gz - anti-HuR rep 5 IgGR5_S8.fastq.gz - control IgG rep 5