Project description:To understand the function of MSI1 in pluripotent stem cells, RNA-seq assays were performed on mouse embryonic stem cells R1, MSI1 knockout cell line R1-C5, human embryonic stem cells H9, RRM knockout cell line H9-C8, MSI1 full-length overexpression cell line H9-MSI1OE, MSI1C variant overexpression cell line H9-MSI1 (138-362) OE , H9-MSI1(272-362)OE. RNA bound by MSI1 in R1 and H9, and MSI1C variants MSI1 (138-362), MSI1(272-362) were detected using RIP-seq.
Project description:Valproic acid (VPA) is a potent inducer of neural tube defects (ntd:s) in both human and mouse, but its mechanism of teratogenicity is not know. The mouse embryonic stem cell line R1, may be relevant as an in vitro model of teratogenicity and was evaluated with exposures to VPA,and the two VPA anlogs (S)-2-pentyl-4-pentynoic acid, and 2-ethyl-4-methyl-pentanoic acid to profile the gene expression response. Those profiles may reveal biomarkers of teratogenic exposures in an in vitro system as well as give mechanistic input of the teratogenicity of VPA.
Project description:Cell line R1 (Mouse embryonic stem cell line) was cultured on 3 different conditions for differentiation study. The experiment ran for 7 days and samples were taken every 24hrs. Afterward, samples on days 0,3,5 and 7 were processed for microarray analysis. The conditions were the differentiation of the stem cells for 7 days through a)formation of embryoid bodies, b)culture on a gelatin coated surface and c) culture on a matrigel coated surface. Keywords: Time course
Project description:A transcriptome study in mouse hematopoietic stem cells was performed using a sensitive SAGE method, in an attempt to detect medium and low abundant transcripts expressed in these cells. Among a total of 31,380 unique transcript, 17,326 (55%) known genes were detected, 14,054 (45%) low-copy transcripts that have no matches to currently known genes. 3,899 (23%) were alternatively spliced transcripts of the known genes and 3,754 (22%) represent anti-sense transcripts from known genes.
Project description:Lipid metabolism is recognized as a key process for stem cell maintenance and differentiation but genetic factors that instruct stem cell function by influencing lipid metabolism remain to be delineated. Here we identify Tnfaip2 as an inhibitor of reprogramming of mouse fibroblasts into induced pluripotent stem cells. Tnfaip2 knockout embryonic stem cells (ESCs) exhibit differentiation failure and knockdown of the planarian orthologue, Smed-exoc3, abrogates in vivo differentiation of somatic stem cells, tissue homeostasis, and regeneration. Tnfaip2 deficient ESCs fail to induce synthesis of cellular triacylglycerol (TAG) and lipid droplets (LD) coinciding with reduced expression of Vimentin (Vim) – a known inducer of LD formation. Knockdown of Vim and Tnfaip2 act epistatically in enhancing cellular reprogramming of mouse fibroblasts. Similarly, planarians devoid of Smed-exoc3 displayed acute loss of TAGs. Supplementation of palmitic acid (PA) and palmitoyl-L-carnitine (a mitochondrial carrier of PA) restores the differentiation capacity of Tnfaip2 deficient ESCs as well as stem cell differentiation and organ maintenance in Smed-exoc3-depleted planarians. Together, these results identify a novel pathway, which is essential for stem cell differentiation and organ maintenance by instructing lipid metabolism.
