Fig. 1: Screening candidate regulatory variants for SLE by SNP-seq.
From: High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus
A Flow chart illustrating the identification of functional candidate SNPs from SLE GWAS data. B SNP-seq: To generate the SNP-seq construct (top), a 31 bp sequence centered on the SNP is positioned between two type IIS restriction enzyme (IIS RE) binding sites. SNPs that fail to bind regulatory proteins such as transcription factors (TF) are negatively selected (bottom), allowing enrichment of protected constructs by PCR. The whole construct can be amplified using primers as per Supplementary Data 9. Bio biotin. Figure 1B was created with BioRender.com released under a Creative Commons Attribution-NonCommerical-NoDerivs 4.0 International license. C The experimental procedure for SNP-seq; NE nuclear extract, Bio biotin. D Spearman’s correlation with a two-tailed test of SNP-seq allele counts normalized to control between PBMC and BL2 samples (ρ = 0.89, P < 1 \(\times\) 10−15). E We selected 248 SNPs that passed next-generation sequencing quality control (NGS-QC) and demonstrated progressive allele-specific protection (Suppl. Fig. 1C). Source data are provided as a Source Data file.
