Processed Sleeping Beauty integration-site and transgene copy-number RNA-seq data for CTCF-insulated vectors in ARPE-19 cells

Processed datasets supporting the manuscript on CTCF-insulated Sleeping Beauty (SB) transposon vectors in ARPE-19 retinal pigment epithelial cells (Cai et al.). This record contains two processed datasets: 1. SB integration-site profiling (manuscript Figures 2B, 2C)Genomic coordinates of unique SB integration sites (hg19/GRCh37, BED format) for the non-insulated vector (sb_wt.bed; 3,860 sites), the single 6xCTCF-insulated vector (CTCF6.bed / s6CTCF; 21,756 sites) and the double 6xCTCF-insulated vector (CTCFD6.bed / dd6CTCF; 27,935 sites), together with a randomized control dataset (random.bed; 16,000 sites). Reads were adaptor- and quality-trimmed (cutadapt, Trimmomatic), aligned with BWA-MEM, processed with SAMtools, and integration sites called from transposon-genome junction reads and collapsed to unique positions. Annotation and coverage profiling used PAVIS and ngs.plot. The randomized control was generated with a Poisson Regression Insertion Model over non-overlapping 20-kb windows. 2. Transgene copy-number RNA-seq (manuscript Figure 6)Transcript-level expression estimates and KEGG pathway enrichment for the comparison of non-insulated ARPE-19 clones carrying low (1-2 copies) versus high (20-31 copies) transgene copy number, with control cells (two biological replicates per condition). Abundances were quantified with Salmon v1.11.4 against a decoy-aware GENCODE v44 index and summarised as TPM; per-gene log2 fold changes were computed from mean TPM (pseudocount 0.1). KEGG over-representation was performed with ShinyGO (FDR < 0.05). Files:- CTCF6.bed, CTCFD6.bed, sb_wt.bed, random.bed - integration-site coordinates (hg19)- gene_expression_results.csv - transcript-level TPM and log2 fold change (low vs high)- enrichment_all.csv, enrichment_top.csv - KEGG pathway enrichment (ShinyGO)- samples.csv - sample-to-condition mapping- README_integration_sites.txt, README_RNAseq.txt - full descriptions Note: this record contains processed data only. Full methods are given in the associated manuscript.