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Rat heart cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

ABSTRACT: Rat somatic heart cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic heart cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic heart cells and rat iPS cells.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE13572 | GEO | 2009/04/01

SECONDARY ACCESSION(S): PRJNA113927

REPOSITORIES: GEO

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Rat lung cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

Project description:Rat somatic lung cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic lung cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic lung cells and rat iPS cells.

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Rat iPS M13 cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

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Gene expression programs between genetically matched PEF and porcine iPSCs

Project description:Somatic cells gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM), and chromatin remodeling has been proved to be involved in this process. To date, chromatin accessibility in porcine induced pluripotency stem cells (piPSCs) was less researched. Here, we explore the connection of chromatin accessibility and transcriptome between genetically matched PEF and piPSCs with high throughput sequencing (ATAC-seq and RNA-seq) approach. In addition, we acquire parent-of-origin chromatin loci and genes after blasting ATAC-seq and RNA-seq data with polymorphic SNP loci which derive from two parental genomes. As a result, we find 4,373 differentially expressed genes (DEGs), and 10,883 differential chromatin locus. Compared with PEF, the closed chromatin loci in piPSCs are tightly connected with the down-expressed genes, while the opened chromatin plays a limited role in the up-regulation of genes. Potential mechanisms of transcription factors (TF) in piPSCs reprogramming have been identified. Moreover, we find 77 parent-of-origin genes and 7 parent-of-origin chromatin loci commonly existed in PEF and piPSC; parent-of-origin chromatin accessibility is not related to the bias expression of RNA. These data reveal regulatory association between global or parent-of-origin chromatin accessibility and transcriptome, which provides new sight to research porcine iPSC reprogramming and genome imprinting.

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Chromatin structure programs between genetically matched PEF and porcine iPSCs

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Rattus norvegicus

Project description:Rat iPS F65 cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

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Project description:Rat iPS M13 cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

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Rattus norvegicus

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Derivation of rat induced pluripotent stem cells that share similarities with embryonic stem cells using a transposon system

Project description:Induced pluripotent stem (IPS) cells have attracted enormous attention due to their vast potential in regenerative medicine, pharmaceutical screening and basic research. The majority of prior established rat IPS cells were generated from somatic cells by retroviral and lentiviral transduction with expression of Oct4, Sox2, Klf4 and c-Myc and using chemical inhibitors of key differentiation pathways. A major difficulty in the application of this technology is the efficient delivery of reprogramming factors and the long-term maintenance of properties of stem cells. Here, we employed the PiggyBac (PB) transposon carrying four 2A peptide-linked reprogramming factors for generating rat IPS cells. These stable rat IPS cells are similar to embryonic stem (ES) cells in morphology, proliferation, teratoma formation, expression characteristic pluripotency markers, developmental potential, and germline transmission. Transcriptional profiling of the IPS cells revealed both pathways in common with ES cells from rat and unique signaling pathway to our cells, including Wnt, TGF and Notch. The cell lines and information obtained in this study will accelerate our understanding of the molecular regulation underlying germline pluripotency and pave the way for exploration of cell-based therapies using the rat.

2012-02-16 | GSE35841 | GEO

Derivation of rat induced pluripotent stem cells that share similarities with embryonic stem cells using a transposon system

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