Additional file 5: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets CS-B35–2, CS-C25–3, CS-C3–2, CS-C32–2, CS-C5–3, CS-3-12, CS-3-14, CS-3-15, CS-3-16 and CS-3-18 Crossover tracts on each chromosome of the maternal P. simonii that were identified in each progeny. Excel Sheet S7 Summary of the crossover numbers on the male chromosomes that were identified in each progeny. Excel Sheet S8 Summary of the crossover events on the male chromosomes that were identified within a short haplotype block region. (XLSX 58 kb

<i>In vitro</i> validation of ¹⁹F-MRI quantification accuracy.

<p>Quantification was validated in a phantom study using cell pellets ranging from 2x10⁵ to 2x10⁶ MSC. Pellets were imaged three times, with the error bars representing the standard deviation between scans. The ¹⁹F-MRI quantification is in very strong agreement with the true number of cells, and has a Pearson correlation coefficient of 0.99. The red line represents the ideal result of a 1:1 correlation.</p

Additional file 4: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets CD-B35–2, CD-C25–3, CD-C3–2, CD-C32–2, CD-C5–3, CD-3-12, CD-3-14, CD-3-15, CD-3-16 and CD-3-18 Crossover tracts on each chromosome of the maternal P. deltoides that were identified in each progeny. Excel Sheet S5 Summary of the crossover numbers on the female chromosomes that were identified in each progeny. Excel Sheet S6 Summary of the crossover events on the female chromosomes that were identified within a short haplotype block region. (XLSX 72 kb

Cellular viability and loading with the ¹⁹F-agent.

<p>(A) Cellular viability was investigated before and after labeling with the ¹⁹F-agent, Cell Sense. Although a statistically significant difference was observed in hMSC after labeling, the viability remained high (>80%) in all experiments. There was no significant difference in mMSC viability. (B) Cellular loading was determined by performing NMR on a known number of cells alongside a reference peak with a known number of ¹⁹F atoms. We observed variation in cellular loading of both hMSC and mMSC between experiments. However, this variation does not affect in vivo ¹⁹F quantification since each transplant was only compared to its specific cellular loading.</p

Representative Day 0 MRI, fluorescence microscopy, and histology acquired as 10x magnification from both implant models.

<p>(A, E) Representative MRI from mice receiving either 2x10⁶ mMSC or 1.5x10⁶ hMSC respectively. The day 0 <i>in vivo</i>¹⁹F-MRI quantification correlates very well with the number of implanted cells. The reference tube is marked by “R”. (B) The red fluorescent fluorine agent is clearly visible in the tissue of the immune competent model, (F) as well as in the immune-compromised model. (C) Furthermore, the GFP+ mMSC are observable within the tissue section. (D) Overlaying the two fluorescent images, reveals the ¹⁹F agent colocalized with the GFP+ mMSC, as expected. (G, H) H&E stained tissue sections corresponding to the fluorescence microscopy clearly show the implant site of the mMSC and hMSC respectively. Scale bars in all images represent 250μm.</p

Additional file 2: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets RD-B35–2, RD-C25–3, RD-C3–2, RD-C32–2, RD-C5–3, RD-3-12, RD-3-14, RD-3-15, RD-3-16 and RD-3-18 Distribution of the number of recombination events over fragment length, which occurred in the meiosis of the female P. deltoides and were identified in each of the 10 progeny. Excel Sheet S1 Distribution of the average number of recombination events over fragment length, which occurred in the meiosis of the female P. deltoides and were identified in the 10 progeny. Excel Sheet S2 Summary of the number and the total length of haplotype blocks in which the maternal recombination events were identified in each progeny. (XLSX 29 kb

Additional file 3: of Identification of recombination events in outbred species with next-generation sequencing data

Excel Sheets RS-B35–2, RS-C25–3, RS-C3–2, RS-C32–2, RS-C5–3, RS-3-12, RS-3-14, RS-3-15, RS-3-16 and RS-3-18 Distribution of the number of recombination events over fragment length, which occurred in the meiosis of the male P. simonii and were identified in each of the 10 progeny. Excel Sheet S3 Distribution of the average number of recombination events over fragment length, which occurred in the meiosis of the male P. simonii and were identified in the 10 progeny. Excel Sheet S4 Summary of the number and the total length of haplotype blocks in which the paternal recombination events were identified in each progeny. (XLSX 29 kb

Additional file 1: of Identification of recombination events in outbred species with next-generation sequencing data

Table S1. Summary of parental blocks from the intermediate files of ‘parent1.abxaa.5snps.blocks’, ‘parent2.aaxab.5snps.blocks’, ‘parent1.long.haplotype’ and ‘parent2.long.haplotype’, created by findGCO. Table S2. The number of SNPs contained in the long parental haplotypes from the intermediate files of ‘parent1.long. Haplotype’ and ‘parent2.long.haplotype’ created by findGCO. Table S3. Distribution of the number of gene conversion events detected in each of the 10 progeny and inherited from the male parent based on the reference genome sequences. Figure S1. CO patterns identified in each progeny on all chromosomes in the female parent P. deltoides. Figure S2. CO patterns identified in each progeny on all chromosomes in the male parent P. simonii. (DOCX 277 kb

Comparison of ¹⁹F-labeled cell detection in two transplantation models over time.

<p>(A) Following implantation of 2x10⁶ mMSC, ¹⁹F-MRI was used to quantify the number of cells remaining over 16 days. By day 16, only 2/7 mice had any detectable signal remaining. A significant difference from day 0 is denoted by <b>+</b>, from day 3 by ◆, and from day 9 by ■. (B) The number of detectable cells over a similar time period following a transplant of 1.5x10⁶ hMSC. ¹⁹F signal was found to decrease at a slower rate, with observable signal in all mice at endpoint. Statistical significance is denoted in the same way as A.</p

Additional file 5: Figure S13. of MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Richards’ growth curves of the 12 QTLs underlying the tree height of Populus, fitted with their genotype values (dot) over time estimated from the multivariate CIM method. The red is for the genotype QQ and the blue for Qq. (PDF 375 kb