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Blood, Vol. 112, Issue 2, 295-307, July 15, 2008
PDGF, TGF-β, and FGF signaling is important for differentiation and growth of mesenchymal stem cells (MSCs): transcriptional profiling can identify markers and signaling pathways important in differentiation of MSCs into adipogenic, chondrogenic, and osteogenic lineages
Blood Ng et al.
112: 295
Supplemental materials for: Ng et al
Human-Ref8 Annotation
Annotation for the Sentrix Human-Ref8 chip (version 1.0) was obtained from the Illumina beadpool manifest file. Annotation of array content is not updated once they are introduced to users. So before performing any data analysis, we updated the Human-Ref8 Refseq annotation using information from the NCBI database. All Refseq IDs are checked to see if they are still valid, replaced, suppressed or terminated and we updated the annotation file accordingly. All IDs that are replaced were updated with the latest Entrez Gene ID while IDs that are suppressed or terminated were removed from our annotation file. Of the 24357 Refseq IDs used in the Human-Ref8 chip, 20731 are still valid or have been replaced by other Refseq IDs. Throughout this paper, the data analyses performed are based on this updated annotation file.
Files in this Data Supplement:
- Table S1. This table shows the average correlation coefficient of triplicate samples in this array (PDF, 19.9 KB) -
Samples of undifferentiated MSC (DMEM and MPRO) and differentiated MSC from these media were run in duplicates and the correlation coefficients (R2) were generated using the entire data of all genes with expression level > 0 or genes with detection confidence > 0.99 or genes with detection confidence >0.99 and expression level > 100 arbitrary units. The correlation coefficients for genes with detection confidence >0.99 range from 0.9787 to 0.9949 and the number of genes is between 8932 to 10485.
- Table S2. Distribution of genes with expression levels <50 and >50 − 10,000 as detected by Illumina bead array in undifferentiated and differentiated MSC populations (PDF, 26.4 KB) -
The cells were grown in DMEM and MPRO and aliquotes from each of these media were differentiated into adipogenic, osteogenic and chondrogenic lineages. In order to compare the distribution of genes in MSC v/s their differentiated progeny the genes from DMEM and MPRO sets were pooled and averaged. This table gives a global overview of transcription where approximately 8000 genes (~80%) were greater than 100 arbitrary units in all samples. This also illustrates that global transcription was similar in undifferentiated MSC as well their differentiated progeny.
- Table S3. Putative MSC markers identified from ANOVA and post hoc analysis (PDF, 55.1 KB) -
Genes highlighted in bold have MSI>1000 on Day 7 and Day 14. Expression profiles of these genes are shown in Figure 1(A).
- Table S4. Putative Adipogenic markers identified from ANOVA and post hoc analysis (PDF, 75.4 KB) -
Genes highlighted in bold have MSI>1000 on Day 7 and Day 14. Expression profiles of these genes are shown in figure 1(B).
- Table S5. Putative Chondrogenic markers identified from ANOVA and post hoc analysis (PDF, 114 KB) -
Expression profiles of these genes are shown in Figure 1(C).
- Table S6. Putative Osteogenic markers identified from ANOVA and post hoc analysis (JPG, 69.2 KB) -
Genes highlighted in bold have MSI>1000. Expression profiles of these genes are shown in Figure 1(D).
- Table S7. Settings in IPA. The row “All IDs” are the numbers of initial input genes (PDF, 15.6 KB)
- Table S8. Primers used for qRT-PCR to evaluate expression of putative MSC and lineage markers (PDF, 39 KB)
- Figure S1. Unsupervised hierarchical clustering of gene expression data allows us to accurately classify MSC (JPG, 154 KB)
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This figure shows a dendrogram of all samples based on experimental conditions. (A) represents samples at day 7, whereas (B) represents samples at day 14.
- Figure S2. Overlap of gene lists between Day 7 and Day 14 (JPG, 84.4 KB)
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Comparisons were made between Entrez Gene IDs used for IPA analysis. The 6 lists above were used as input into IPA.
- Figure S3. Selected pathways comparison between all 3 lineages of MSC differentiation (JPG, 65.3 KB)
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The bar charts shows the number of up/down-regulated genes in each sample. The red portion represents up regulation whereas the green portion represents down regulation.
- Figure S4. Changes in TGF-β signaling during MSC differentiation (JPG, 108 KB)
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The green components are downregulated & the red components are upregulated during differentiation as compared to undifferentiated MSC. The intensity of the color is directly proportional to the differential expression of that gene.
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