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Blood, Vol. 113, Issue 22, 5434-5443, May 28, 2009
Sustained high-level polyclonal hematopoietic marking and transgene expression 4 years after autologous transplantation of rhesus macaques with SIV lentiviral vector–transduced CD34+ cells
Blood Kim et al.
113: 5434
Supplemental materials for: Kim et al
Files in this Data Supplement:
- Table S1. Primers for LAM–PCR (XLS, 14 KB)
- Table S2. All inserrtions with CIS (XLS, 110 KB)
- Table S3. Comparison of SIV experimental and random 10,000 datasets using bootstrapping analysis (XLS, 13.5 KB)
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The table gives the p values that the number of hits observed occurred by chance, and the false discovery rate (FDR) to correct the inflated Type I error rates that correspond to different number of hits. The sampling size for Bootstrapping was 30 from both experimental and computer-generated random datasets, chosen to be large enough to satisfy the law of large numbers and the central limit theorem so that repeated samples will have a Gaussian or (normal) distributions. References for this methodology are given below.
1. Davison, A.C.; Hinkley, D. Bootstrap Methods & their Applications. (2006). Bootstrap Methods and their Applications, 8th, Cambridge Series in Statistics and Probabilistic Mathematics.
2. Effron, B.;Tibshirani, R. (1993). An Introduction to the Bootstrap. Chapman & Hall/CRC.
3. Chernick, Michael R. (1999). Bootstrap Methods, A Practioner’s guide. Wiley Series in Probability and Statistics.
- Figure S1. Long-term vector expression in numerous hematopoietic cell subsets in the PB and BM of transplanted animals (JPG, 80.5 KB)
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The percentage of various GFP expressing hematopoietic cell types as defined by immunophenotyping of peripheral blood and BM in animals RQ3356 and RQ2617 four years following transplantation.
- Figure S2. Distribution of SIV integrations and in silico “random” datasets around transcription start sites (TSS) (JPG, 113 KB)
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Short-term: SIV insertions in granulocytes 6–12 months following transplantation. Long-term: SIV insertions in granulocytes 35–47 months post-transplantation. SIV all: pooled short-term and long-term insertions. Randoms: 10,000 sets of matched in silico coordinates as explained in Materials and Methods.
- Figure S3. Distribution of SIV integrations and in silico “random” integrations within genes (JPG, 95.1 KB)
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For each integration site within a gene, we found the distance between the integration site and the 5′ end of the transcript, as well as the length of the transcript (in genomic coordinates). We broke each gene into ten equal sections and calculated which bin the integration site mapped to. bin1 is closes to the TSS, and bin10 is farthest away. If an integration site is within the intron of two different genes, we randomly picked one of those genes for the analysis. Early: SIV insertions in granulocytes 6–12 months following transplantation. Late: SIV insertions in granulocytes 35–47 months post-transplantation. All SIV: pooled short-term and long-term insertions. Randoms: 10,000 sets of matched in silico coordinates as explained in Materials and Methods.
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