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Genome-wide transcriptome analyses by the RNA-seq method

ABSTRACT: We performed the whole transcriptome analysis in Zscan4 positive ES cells (Em+) and Zscan4 negative ES cells (Em-) by using FACS-sorted MC1-ZE7 ES cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE58619 | GEO | 2015/09/10

SECONDARY ACCESSION(S): PRJNA253029

REPOSITORIES: GEO

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Genome-wide transcriptome analyses by the RNA-seq method

Project description:We performed the whole transcriptome analysis in Zscan4 positive ES cells (Em+) and Zscan4 negative ES cells (Em-) by using FACS-sorted MC1-ZE7 ES cells. Whole RNA-seq in Zscan4 positive and negative cells

2015-09-10 | E-GEOD-58619 | biostudies-arrayexpress

ChIP-seq assays for H3K9me2

Project description:We analyzed the genome-wide chromatin states in Zscan4 positive ES cells (Em+) and Zscan4 negative ES cells (Em-) by using FACS-sorted MC1-ZE7 ES cells. H3K27 hyperacetylation and DNA demethylation were detected in heterochromatic regions of Em+ cells. These results suggested that the heterochromatin is activated in Zscan4 positive state.

2015-09-10 | GSE58617 | GEO

ChIP-seq assays for H3K9me2

2015-09-10 | E-GEOD-58617 | biostudies-arrayexpress

ChIP-seq assays for H3K27ac

Project description:By using FACS-sorted MC1-ZE7 ES cells, we analyzed the genome-wide distribution of H3K27ac and DNA methylation in Zscan4 positive ES cells (Em+) and Zscan4 negative ES cells (Em-). H3K27 hyperacetylation and DNA demethylation were detected in heterochromatic regions of Em+ cells, but not Em- cells. These results suggested that the Zscan4 state takes "open" chromatin conformation in ES cells. H3K27ac in Zscan4 positive and negative cells

2015-09-10 | E-GEOD-51679 | biostudies-arrayexpress

ChIP-seq assays for H3K27ac

2015-09-10 | GSE51679 | GEO

Genome-wide DNA methylation analyses by the MeDIP assay

Project description:We analyzed the genome-wide DNA methylation in Zscan4 overexpressing ES cells. Zscan4 overexpression induced slight DNA demethylation in telomere and major satellite regions. Subsequent genome-wide analysis of non-repeated regions revealed the significant reduction of DNA methylation at Zscan4-dependent hyperacetylation sites. This result indicates that Zscan4 is not only a marker of the Zscan4+ state of ES cells, but also indispensable for the dramatic epigenetic modifications occurring in the Zscan4+ state. DNA methylation in Zscan4 overexresssing ES cells

2015-09-10 | E-GEOD-58618 | biostudies-arrayexpress

Genome-wide DNA methylation analyses by the MeDIP assay

2015-09-10 | GSE58618 | GEO

RNAseq Data of Neural Stem Cells, Glial progenitors and Sox1 positive Glial progenitors

Project description:With this study we aimed to characterize the changes invoked in glial progenitor cells by activation of the endogenous copy of the master transcription factor Sox1. For this study, a progenitor cell line was derived from ES cells carrying a heterozygous GFP knock-in in the Sox1 ORF. Sox1 positive cells were identified by GFP expression, and separated by FACS. As control population, Sox1 negative progenitors were used, as well as GFP sorted and unsorted, Sox1 positive Neuroepithelial cells derived from the same ES cell line.

2019-04-18 | GSE119480 | GEO

RNAseq comparison of gene expression profiles in ScxGFP positive cells and ScxGFP negative cells from E13.5 forelimb samples

Project description:RNAs were isolated from FACS sorted ScxGFP positive cells and GFP negative cells of forelimbs at E13.5, and characterized by RNAseq

2015-03-19 | GSE65177 | GEO

The effect of cell subset isolation method on gene expression in leukocytes.

Project description:Analysis of the effect of isolation methods (fluorescence activated cell sorting (FACS), positive and negative immunomagnetic selection) on gene expression in human primary CD4+, CD8+ T cells, B cells and monocytes. FACS incurs the least short-term changes in gene expression signature.

2013-08-20 | GSE50008 | GEO

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