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PKHD1-deficient human induced pluripotent stem (iPS) cell-derived cholangiocyte-like cells (PKHD1-KO CCs) vs heterozygously mutated PKHD1 human iPS cell-derived cholangiocyte-like cells (PKHD1-Hetero CCs)

ABSTRACT: Transcriptional profiling of PKHD1-KO and PKHD1-Hetero CCs. PKHD1-deficient (PKHD1-KO) and heterozygously mutated PKHD1 iPS clones were established by RNA-guided genome editing using CRISPR/Cas9 system. The iPS clones were differentiated into cholangiocyte-like cells in cysts (cholangiocytic cysts, CCs) in a 3D-culture system.

ORGANISM(S): Homo sapiens

PROVIDER: GSE125871 | GEO | 2019/03/19

REPOSITORIES: GEO

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PKHD1-deficient human induced pluripotent stem (iPS) cell-derived cholangiocyte-like cells (PKHD1-KO CCs) vs heterozygously mutated PKHD1 human iPS cell-derived cholangiocyte-like cells (PKHD1-Hetero CCs)

Project description:PKHD1-deficient human induced pluripotent stem (iPS) cell-derived cholangiocyte-like cells (PKHD1-KO CCs) vs heterozygously mutated PKHD1 human iPS cell-derived cholangiocyte-like cells (PKHD1-Hetero CCs)

| PRJNA517738 | ENA

Gene expression profiles of murine fibroblasts and iPS

Project description:We reprogrammed adult murine fibroblasts obtained from p14f/f (wt version of conditional loxP-flanked p14 knockout (KO); C57/Bl6) by transduction of a lentiviral vector (pRRL.PPT.SF.hOKSMco.idTom.PRE) overexpressing the four Yamanaka factors (c-Myc, Klf-4, Oct-4, Sox-2). After successful reprogramming and establishment of stable iPS clones we performed gene expression profiling of three different murine iPS clones (#2, #2EX, #3) and their parental fibroblasts.

2018-03-01 | GSE97152 | GEO

LEOPARD Syndrome iPS, BJ iPS and Fibroblasts

Project description:Expression data from LEOPARD Syndrome-iPS clones, BJ-iPS cells and parental Fibroblasts

2010-06-10 | GSE20473 | GEO

DNA microarrays of three shRNA control iPS clones (Ctrl 2,3,4) and shECAD iPS clones (shECAD 4,8,9)

2010-06-01 | GSE21062 | GEO

RNA-seq of CD34+CD43+ cells derived from CMML-iPS clones and Control-iPS clones

Project description:RNA-seq of CD34+CD43+ cells derived from CMML-iPS clones and Control-iPS clones for integration with eRRBS analysis

2020-04-30 | E-MTAB-7850 | biostudies-arrayexpress

Global transcriptome profiling of Oct4/Klf4/Sox2 (3Factor, 3F) + IL6 iPS clones derived from mouse embryonic fibroblasts.

Project description:We used heterokaryon cell fusion based reprogramming and identified the cytokine IL6 as a potential regulator of reprogramming to pluripotency. We generated iPS clones using the four reprogramming factors (4F) Oct4, Klf4, Sox2, and c-Myc. In addition, iPS clones were generated using only three factors (3F: Oct4, Klf4, amd Sox2) with the addition of the cytokine IL6 to reprogramming culture conditions. Global RNA-Seq of the 3F + IL6 derived iPS clones was done for comparison with 4F-derived iPS clones, mouse embryonic stem cells and mouse embryonic fibroblasts.

2013-08-28 | GSE46104 | GEO

DNA microarrays of three shRNA control iPS clones (Ctrl 2,3,4) and shECAD iPS clones (shECAD 4,8,9)

Project description:E-cadherin upregulation is an early event of reprogramming of fibroblasts to induce pluripotent stem cells (iPS). Knocking down of E-cadherin by shRNA impairs iPS generation, though some colonies with great morphorlogical difference to shRNA control colonies remain. To illustrate the molecular and functional difference between shECAD iPS clones and shRNA control iPS clones, three respective iPS clones (shECAD 4,8,9 and Ctrl 2,3,4) were derived and DNA microarrays were run to analyze the transcriptional profile of these clones. OG2 MEFs were infected with Sox2, Klf4, Oct4 and c-Myc (SKOM) plus either Luciferase shRNA (shLUC) or E-cadherin shRNA (shECAD) retrovirus. At Day 6 post infection cells were split onto feeder cells. Several colonies from SKOM+shLuc and SKOM+shECAD were picked out at Day 14 post infection respectively and three cell lines were established, namely Ctrl 2,3,4 for SKOM+shLuc iPS and shECAD 4,8,9 for SKOM+shECAD iPS. All clones were maintained on feeder cells in mESC medium. RNA were extracted from these six cell lines and DNA microarrays were run to analyze the transcriptional profile.

2010-06-08 | E-GEOD-21062 | biostudies-arrayexpress

mRNA expression in iPS cells generated by a synthetic self-replicative RNA

Project description:We generated iPS cells with a synthetic self-replicative RNA that expresses four independent reprogramming factors (OCT4, KLF4, SOX2 and either c-MYC or GLIS1). We performed whole genome RNA sequencing (RNA-seq) of iPS cell clones, parental BJ and HUES9 ES cell controls. All iPS cell clones analyzed by RNA-seq showed unsupervised hierarchical clustering and expression signatures characteristic of human HUES9 ES cells that were highly divergent from parental human fibroblasts.

2014-04-25 | GSE38265 | GEO

Effect of Aid deletion on the global gene expression iPS cells

Project description:It has been shown that DNA demethylation has a pivotal role in the generation of induced pluripotent stem (iPS) cells. However, the underlying mechanism is still unclear. Previous reports indicated that activation-induced cytidine deaminase (Aid) is involved in DNA demethylation in several developmental processes and cell fusion-mediated reprogramming. Based on the reports, we hypothesized that Aid may be involved in DNA demethylation during the iPS cell generation. In this study, we examined the function of Aid in iPS cell generation using Aid knockout (Aid-/-) mice expressing a GFP reporter under the control of a pluripotent stem cell marker, Nanog. By the introduction of Oct3/4, Sox2, Klf4 and c-Myc, Nanog-GFP positive iPS cells could be generated from the fibroblasts and primary B cells of Aid-/- mice. The Aid-/- iPS cells showed normal proliferation and gave rise to chimeras, indicating their capacity for self-renewal and pluripotency. Microarray analysis demonstrated that the global gene expression of Aid-/- iPS cells was similar to that of Aid+/+ iPS cells. Aid+/+ and Aid-/- iPS colonies were generated from Aid+/+ and Aid-/- MEFs and picked up mechanically. The clones were passaged four times on feeder cells and two times on gelatin-coated dishes to exclude the contamination of feeder cells. Subsequently, the RNA was isolated. Six Aid+/+ iPS cell clones and six Aid-/- iPS cell clones were compared by microarray.

2014-04-10 | GSE51955 | GEO

LEOPARD Syndrome iPS, BJ iPS and Fibroblasts

Project description:Expression data from LEOPARD Syndrome-iPS clones, BJ-iPS cells and parental Fibroblasts 9 samples in total are analyzed. Among 22011 genes in expression data, there are 3657 genes with at least 2 fold expression change between the average of the three fibroblast lines versus all of the iPS lines/HES samples. A heatmap can be generated for the expression levels for the 3657 genes and 9 samples.

2010-06-24 | E-GEOD-20473 | biostudies-arrayexpress

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