File S1 - An Improved SELEX-Seq Strategy for Characterizing DNA-Binding Specificity of Transcription Factor: NF-κB as an Example

Supporting figures and tables. Figure S1. Contribution of cytosine after the binding site of GGGACTTTCC to the DNA binding affinity of NF-κB. A, all 16-mer sequences containing the site of GGGACTTTCC were collected from reads of Round 4 and classified according to the nucleotides flanking the end of the site. B, EMSA analysis of the relative binding affinities of NF-κB p50 to two dsDNA probes of agttgagGGGACTTTCCTaggc (a) and agttgagGGGACTTTCCCaggc (b). C, the quantified signal intensity of the shifted band. The ends of two dsDNA probes were labeled with biotin. The protein-binding reactions and the EMSA protocol were same as described in Materials and Methods. Figure S2. NF-κB p50 protein was separated by SDS-PAGE and visualized by silver staining. Molecular weight marker (MW marker) was indicated on the left. Table S1. Oligonucleotides designed for SELEX. Table S2. NF-κB motifs reported by other studies. Table S3. Three motifs obtained with reads of Round 3 and 4. Table S4. Enrichments of three motifs obtained with the reads of Round 3 and 4. Table S5. Enrichments of 10 sequences (10-mer) in SELEX-Seq and the relative affinities determined by EMSA. (DOC)