Project description:The transcriptional response of normal and glioblastoma-derived neural (GNS) cells was profiled in self-renewing conditions and over a time course of differentiation in the presence of bone morphogenic protein (BMP).
Project description:Glioblastoma-derived neural stem (GNS) cells were reprogrammed to induced pluripotent stem (iPS) cells by transgenic expression of OCT4 and KLF4. Genome-wide DNA methylation status was profiled at 27,578 CpG sites to assess epigenetic erasure and restoration due to reprogramming and redifferentiation to the neural stem (NS) cell state.
Project description:Glioblastoma-derived neural stem (GNS) cells were reprogrammed to induced pluripotent stem (iPS) cells by transgenic expression of OCT4 and KLF4. Genome-wide DNA methylation status was profiled at 485,000 loci to assess epigenetic erasure and restoration due to reprogramming and redifferentiation to the neural stem (NS) cell state.
Project description:Glioblastoma-derived neural stem (GNS) cells were reprogrammed to induced pluripotent stem (iPS) cells by transgenic expression of OCT4 and KLF4. Genome-wide DNA methylation status was profiled at 485,000 loci to assess epigenetic erasure and restoration due to reprogramming and redifferentiation to the neural stem (NS) cell state.
Project description:Chromatin accessibility was profiled by ATAC-seq in normal and glioblastoma-derived neural stem (GNS) cells, in self-renewing conditions and in response to differentiation stimulus with bone morphogenic protein (BMP).
Project description:BRD4 is an important epigenetic reader implicated in the pathogenesis of a number of different cancers and other diseases. Brd4-null mouse embryos die shortly after implantation and are compromised in their ability to maintain the inner cell mass (ICM), which gives rise to embryonic stem cells (ESCs). We investigated the functions of Brd4 in the ESCs in the present study. To determine the Brd4 target genes in embryonic stem cells. TL1 ESCs were transfected with control siRNA, or Brd4 siRNA. At 48 h post-transfection, total RNAs were isolated using the RNeasy minikit (Qiagen). Expression microarray analyses were performed on mRNA samples isolated from three independent experiments using a mouse Gene 2.0ST array (Affymetrix) at the University of Pennsylvania Microarray Core Facility. RMA from Affymetrix package was applied to the data for preprocessing and normalization. Limma was used for detection of differentially expressed genes. Benjamini & Hochberg correction was applied for the multiple comparisons.
Project description:Enteric glial cells (EGCs) are the main constituent of the enteric nervous system and share similarities with astrocytes from the central nervous system including their reactivity to an inflammator microenvironment. In this study we isolated GFAP-positive myenteric glia from FVB/hGFAP-eGFP transgenic postnatal day 7 mice. Following cell sorting for the eGFP reporter, GFAP-positive EGCs were cultured for 3 weeks to generate neurosphere-like bodies. This cell culture was stimulated with LPS for 48 h and cells were employed for gene expression profiling. LPS-stimulated cell cultures were compared to untreated control cell cultures. Enriched GFAP+ EGC cultures secreted increased levels of prominent inflammatory cytokines upon LPS stimulation. Further, in vitro cultures were compared to GFAP-eGFP-positive cells directly analyzed after cell sorting of small intestinal LMMP digests (in vivo) to assess alterations in transcriptomic profiles due to the in vitro culture. In vivo data and in vitro data were collected in three independent replicates. For each replicate one litter of FVB/hGFAP-eGFP transgenic mice at postnatal day 7 was employed. GFAP-eFP-positive small intestines were digested enzymatically and from the single cell suspensions eGFP-positive GFAP-expressing cells were sorted by fluorescence-activated cell sorting. For the in vivo data the cells were directly sorted into lysis buffer and further processed . For the in vitro data GFAP-eGFP cells were seeded onto coated plastic dishes for adherent growth and cultured in DMEM/F12-medium supplemented with antibiotics, N2, B27, bFGF and EGF. In the first passage cells were divided into two uncoated six well dishes to promote spheroid growth. One well was supplemented with LPS (100 µg/ml, from E. coli O26:B6, Sigma Aldrich, potency 3 EU/ng) for 48 h, the corresponding second well was left untreated and used as respective control. After 48 h, cells were processed for total RNA isolation.