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These findings for STS mRNA expression levels in relation to genotype in brain tissue therefore require further investigation, preferably using a more cell specific approach such as laser capture micro-dissection techniques.
Future studies in the context of gene expression should aim towards more cell specific assays, with the goal to find the genes directly related to lesion formation versus genes responsible for initiating defenses further away in the leaf and in systemic tissues.
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However, we cannot discard the possibility that those for which we did not observe any phenotype could be involved in more cell-specific roles that we could not discriminate at the gross morphological level.
Future studies should address the expression of HGF and KGF in a more cell-specific fashion.
Intriguingly, there is also evidence that hypoxia-responsive miRNAs may be regulated in a more cell-specific manner.
However it remain possible that small expression changes in oligodendrocytes could be masked by secondary neuronal death and dysfunction and more cell-specific expression studies are necessary.
More cell type specific co-occuring TF motifs can be found in Additional file 3.
Work in many cell types describes HIF-1α as constitutively hypoxia-regulated and HIF-2α as more cell type specific, its transcriptional activation being influenced by micro-environmental conditions other than hypoxia [ 30, 31].
Similar enrichment was also seen for lncRNAs, although the enrichment was more cell type-specific, supporting the characteristic attribute of lncRNAs as cell type-specific transcripts.
To further confirm this, we performed hierarchical clustering using all ATAC-seq samples and again obtained better separation among tissues compared to that using RNA-seq data, suggesting that ATAC-seq data contains more cell type-specific information to detect the diversity in MSCs (Fig. 4c).
Since we expect more cell type-specific data to be generated on TF binding and chromatin structures, our perspective of dynamic CRM occupancy will only become more complex.
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