Project description:Gene expression study of shRNA knockdown of GATA1 in the megakaryoblastic cell line Meg01. Cell culture samples from two Meg01 clones (GATA1 4-14 and GATA1 5-13) were compared against a negative control infection sample (GATA1-neg). Two dye-swap microarrays were completed for each clone.
Project description:chIP-on-chip analysis of GATA1 in the megakaryoblastic cell line Meg01. The IP was obtained with a GATA1 C-terminus antibody. The control sample was a normal goat IgG pull down done side by side with the GATA1 (C-20) antibody using the same soluble chromatin sample from non-treated Meg-01 cells. A 2-chip microarray set (Agilent 240K) was used for the chIP-on-chip analysis.
Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression.
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes
