Transcriptome data for human ES, IMR90 and IMR90-derived iPS (ESIMR90) cells
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ABSTRACT: Assessing relevant differences between human induced pluripotent stem (iPS) cells and human embryonic stem (ES) cells is important, given that such differences may impact their potential therapeutic use. We used microarray to profile the changes in global gene expression arising from the reprogramming of somatic cells to induced pluripotent stem cells. Comparison of gene expression between human embryonic stem cells (HES-3), induced pluripotent stem cells (ESIMR90) and its parental fibroblasts (IMR90). A pair of biololical replicates were analysed for each cell line.
Project description:Assessing relevant differences between human induced pluripotent stem (iPS) cells and human embryonic stem (ES) cells is important, given that such differences may impact their potential therapeutic use. We used microarray to profile the changes in global gene expression arising from the reprogramming of somatic cells to induced pluripotent stem cells. Comparison of gene expression between human embryonic stem cells (HES-3), induced pluripotent stem cells (ES4SKIN) and its parental fibroblasts (FORESKIN). A pair of biololical replicates were analysed for each cell line.
Project description:Assessing relevant differences between human induced pluripotent stem (iPS) cells and human embryonic stem (ES) cells is important, given that such differences may impact their potential therapeutic use. We used microarray to profile the changes in global gene expression arising from the reprogramming of somatic cells to induced pluripotent stem cells.
Project description:Pluripotent stem cells, including human embryonic stem (hES) and human induced pluripotent stem (hiPS) cells, have been regarded as potential sources for cell-based transplantation therapy. However, the immunogenicity of these cells remains the major determinant for successful clinical application. We therefore studied multiple hES and hiPS cell lines for MHC expression, HLA haplotyping, expression of immune-related genes and T cell activation. The data showed lower levels of MHC class I (MHC-I), b2-microglobulin and HLA-E in undifferentiated stem cells, but the levels were increased to near the levels of somatic cells after co-treatment with interferon gamma. However, the percentages of cells expressing antigen presenting cell markers and MHC-II molecules remained consistently low. Activation of responder lymphocytes by the pluripotent stem cells was significantly lower than by allogeneic lymphocytes in mixed lymphocyte reactions. Finally, the data showed significant differential expression of immune privilege genes (TGF-beta2, Arginase 2, Indo1, GATA3, POMC, VIP, CACLA, CACLB, IL-1RN, CD95L, CR1L, Serpine 1, HMOX1, IL6, LGALS3, HEBP1, THBS1, CD59 and LGALS1) between pluripotent stem cells/derivatives and somatic cells. We concluded that pluripotent stem cell progeny may retain some level of immune privilege and will likely behave in a way different from those of somatic cells after transplantation. Confirmed hiPSC cells and their parental cells were selected for RNA extraction and Affymetrix array analysis. To minimize the clone variation, we selected two clones from each type of iPSC.
Project description:Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a. In this study, we have screened for shRNAs blunting reprogramming-induced senescence. To investigate the effects of OSKM expression on the transcriptome of human primary IMR90 fibroblasts, we performed RNA-sequencing (RNA-Seq). Cells were transduced with OSKM expression or control vector and RNA was extracted after 14 or 20 days. In addition, to study the transcriptome of cells bypassing OSKM-induced senescence due to p21 or mTOR depletion, we performed RNA-seq of cells transduced with OSKM and shRNA expressing vectors targeting p21 or mTOR for 14 or 20 days.
Project description:DNA methylation was measured by MBD2 enrichment of DNA fragments in IMR90. A statistical model was developed to estimate absolute methylation levels, and compared to whole genome bisulfite sequencing results (Lister, R. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature) Two techincal replicates of MBD2 methylated DNA enrichment in IMR90 cells.
Project description:IMR90 cells were passaged until replicative senescence and compared with proliferating cells. We used RNA-Seq to detail the global programme of gene expression in human IMR90 replicative induced senescence
Project description:IMR90 cells were infected with pLNC-RAS:ER (from Jesus Gil lab) with retroviral gene transfer. Infected cells were drug selected G418. The cells were induced either with ethanol as control or with 100nM final conc 4-hydroxytamoxifen (sigma H7904) for ectopic expression of protein We used RNA-Seq to detail the global programme of gene expression in human IMR90 oncogene induced senescence
Project description:SMEI patient induced pluripotent stem cells (iPSCs) were derived from patient fibroblasts. In order to test the similarity between patient iPSCs and human embryonic stem (hES) cells, microarry analysis was carried out on SMEI patient iPSCs and human embryonic stem cells.