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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE21062 | GEO | 2010/06/01

SECONDARY ACCESSION(S): PRJNA129681

REPOSITORIES: GEO

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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

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

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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

| PRJEB32099 | ENA

Whole genome sequencing of murine induced Pluripotent Stem (iPS) cell clones

Project description:Whole genome sequencing was performed on several murine iPS cell clones (and their parental cells) from each of three independent reprogramming experiments. Hundreds of single nucleotide variants (SNVs) were detected in each clone, with an average of 11 in coding regions. Affymetrix Mouse Exon 1.0ST arrays were used to compare expression patterns in MPSVII iPS lines, and embryo-derived MPSVII ES cells. Unsupervised hierarchal clustering analysis showed that the iPS clones and ES cell lines clustered randomly, suggesting that their global patterns of gene expression are highly similar. Taken together, our data suggest that most of the genetic variation in iPS cell clones is not caused by reprogramming, but is rather a consequence of cloning individual cells, “capturing” random mutations that preexisted in the single cells that were reprogrammed. These mutations can sometimes contribute to reprogramming “fitness”, thus providing a selective advantage for rare cells when they overexpress reprogramming factors.

2012-03-15 | GSE36017 | GEO

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.

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Molecular mechanisms underlying reprogramming of mouse fibroblasts into pluripotent stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE21062: DNA microarrays of three shRNA control iPS clones (Ctrl 2,3,4) and shECAD iPS clones (shECAD 4,8,9) GSE21064: DNA microarrays of SKOM transduced MEFs with added Tgfb1 or co-expressing Snail Refer to individual Series

2010-06-08 | E-GEOD-21067 | biostudies-arrayexpress

Mus musculus

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

| PRJNA129681 | ENA

Whole genome sequencing of murine induced Pluripotent Stem (iPS) cell clones

2012-03-15 | E-GEOD-36017 | biostudies-arrayexpress

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

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

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