Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

Supporting Information for Hickey et al., 2015

Supporting Information

  • Supporting Information - Figures S1-S8, Tables S1-S2, descriptions of Files S1-S9, and File S10 (PDF, 3 MB)
  • Figure S1 - Sequences of primers/oligonucleotides used in the generation of Tf1 serial number data in sap1+ and sap1-1 cells. (PDF, 889 KB)
  • Figure S2 - The sap1-1 mutation causes no apparent growth defect at 25°C. (PDF, 756 KB)
  • Figure S3 - The majority of Tf1 integration occur in regions of the genome that are bound by Sap1. (PDF, 818 KB)
  • Figure S4 - The pattern of Tf1 insertions at specific nucleotide positions near Sap1 binding motifs is not altered in sap1-1 yeast. (PDF, 648 KB)
  • Figure S5 - Error rate in reading the eight base pair serial number sequence. (PDF, 780 KB)
  • Figure S6 - The distortion function between two serial numbers as a function of the number of base differences between them. (PDF, 806 KB)
  • Figure S7 - (A) Number of positions in each of the datasets versus the number of raw serial number at the position. (B) Number of average duplicates per serial number at a position versus the number of raw serial numbers at the position. (PDF, 606 KB)
  • Figure S8 - (A) Proportion of positions that could be analyzed by the rate distortion method versus the number of raw serial numbers at the position. (B) Average proportion of serial numbers judged as not real at a position by the rate distortion method versus the number of raw serial numbers at the position. (PDF, 1 MB)
  • Table S1 - List of computer programs and scripts used in this study (available upon request). (PDF, 490 KB)
  • Table S2 - Tf1 insertion numbers relative to genomic regions of Sap1 binding (Log2 Ratio of Sap1/WCE > 0). (PDF, 459 KB)
  • File S10 - Supplemental Methods (PDF, 925 KB)
  • File S1 - Integration sites for sap1+ (32°C) replica #1. (.txt, 7 MB)
  • File S2 - Integration sites for sap1+ (32°C) replica #2. (.txt, 5 MB)
  • File S3 - Integration sites for sap1+ (32°C) replica #3. (.txt, 4 MB)
  • File S4 - Integration sites for sap1+ (25°C) replica #1. (.txt, 5 MB)
  • File S5 - Integration sites for sap1+ (25°C) replica #2. (.txt, 5 MB)
  • File S6 - Integration sites for sap1+ (25°C) replica #3. (.txt, 6 MB)
  • File S7 - Integration sites for sap1-1 (25°C) replica #1. (.txt, 3 MB)
  • File S8 - Integration sites for sap1-1 (25°C) replica #2. (.txt, 3 MB)
  • File S9 - Integration sites for sap1-1 (25°C) replica #3. (.txt, 3 MB)