Project description:The experiment was designed to unravel how endogenous signaling in differentiating hESCs is affected by exogenous factors. RNA-seq of human ES cell lines HUES4 and H1, differentiated for 5 or 7 days towards pancreatic endoderm. The cells were treated with IWP-L6, TGFb1 or both from day 3 and onwards. Vehicle controls were done with 0.1% DMSO.
Project description:To investigate the difference of mRNA and lncRNA profiling between cisplatin-resistance and regular T24 bladder cancer cells, T24 cells were treated with a gradual increment (4, 8, 16, 32, 64 ug/ml cisplatin) with a discontinuous period until cells recover. 10^6 cells T24R and T24 cells were harvested for RNA-seq.
Project description:To better understand the mechanism by which HES1 regulates pancreas development we took advantage of recent developments in directed differentiation of human embryonic stem cells (hESCs) to the pancreatic endocrine lineage via a series of progenitor stages (Figure 1 and (Rezania et al., 2014). Using the iCRISPR platform (González et al., 2014), we introduced indels in the HES1 and NEUROG3 genes, either singly or in combination in iCRISPR H1 cells. Using previously described gRNAs (Zhu et al., 2016) to target exon2 of the NEUROG3 gene and exon2 of the HES1 gene we detected by Sanger and RNA-sequencing a 2 bp insertion and a T insertion, respectively, resulting in premature STOP codons in two/multiple clonal cell lines carrying the introduced mutation and the loss of NEUROG3 by immunostaining We then subjected two or more clonal lines of H1-iCRISPR (wildtype), HES1−/−, NEUROG3−/− and HES1−/−NEUROG3−/− (abbreviated H1N3-dKO or H1−/−N3−/−) to differentiation to β-like cells using a modified version of the protocol from Rezania et al. (2014). Marker analysis showed that all cell lines maintained pluripotency (OCT4+) as hESC and were able to differentiate to FOXA2+ and SOX17+ co-positive definitive endoderm (DE, Day 3), PDX1+ cells at the posterior foregut stage (PF, Day 7), to bipotent progenitors marked by PDX1+ and NKX6-1+ at the Pancreatic Endoderm stage (PE, Day 10), and the Endocrine Precursor stage (EP, Day 13)
Project description:TNFα is a potent cytokine to mediate inflammatory response by activation of the master transcription factor NF-kB. Endothelial cells are important participants in inflammatory responses in animals. NF-kB is a major mediator to activate endothelial cells by inducing multiple pro-inflammatory genes in response to TNFα. NF-kB mediated gene transcription is known to accompany rapid changes in epigenetic states. However, the epigenetic landscape in response to the cytokine challenge TNFα in mouse endothelial cells has not been described. Our approach characterized the epigenetic profiles on a genome-wide scale and mapped putative active enhancers in primary mouse aortic endothelial cells.
Project description:To identify the role of BLIMP1 in Waldenström's macroglobulinemia, the PRDM1 transcript was targeted using an artificial miRNA. RNAseq was used to compare it to a non-targeting control in the RPCI-WM1 cell line. To determine the role of EZH2 in Waldenström's macroglobulinemia, the RPCI-WM1 cell line was treated with 0.3µM of the EZH2 inhibitor Tazemetostat, compared to DMSO vehicle control by RNAseq. ChIPseq was performed for the factors BLIMP1 and H3K27me3 in the RPCI-WM1, OPM-2 and NCI-H929 cell lines, along with ChIPseq for EZH2 in the NCI-H929 cell line.
Project description:RNA-seq to clarify the molecular mechanism by which a mesodermal transcription factor, T/Brachyury, disrupts the defined naive pluripotency and induce the concomitant differentiation program.
Project description:Recently, direct reprogramming between divergent lineages has been achieved by introducing cell-fate-determining transcription factors. This progress may provide alternative cell resources for drug discovery and regenerative medicine. However, the genetic manipulation may limit the future application of these approaches. In this study, we identified a novel small-molecule cocktail that directly converted fibroblasts into neuronal cell fate with a high yield up after 16-days of induction. After a further maturation stage, these chemically-induced neurons (CiNs) possessed neuron-specific expression patterns, generated action potentials and formed functional synapses. Gene expression profiling revealed the activation of neuronal specific genes in the early stage of small molecule treatment. Overall, our findings prove the principle of chemically-induced direct reprogramming of somatic cell fates across germ layers without genetic manipulation, and show that cell fate can be manipulated through disrupting initial cell program and activating target cell master genes with pure chemicals. Total of 15 samples were analyzed, including mouse fibroblasts, mouse cortical primary neurons and chemically-induced neurons by different duration of chemical induction (Day0, Day4, Day8, Day19) and different small-molecule cocktail (FICB, FICB-1)