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Unknown,Transcriptomics,Genomics,Proteomics

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MRNA-Seq of 2C::tomato+ vs. - ES cells

ABSTRACT: We identified/quantified genes and repeat elements enriched within 2C::tomato+ cells vs. 2C::tomato - cells 2C::tomato + and - cells were collected by FACS for RNA-Seq analysis

ORGANISM(S): Mus musculus

SUBMITTER: Todd Macfarlan

PROVIDER: E-GEOD-33920 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Embryonic stem cell potency fluctuates with endogenous retrovirus activity.

Macfarlan Todd S TS Gifford Wesley D WD Driscoll Shawn S Lettieri Karen K Rowe Helen M HM Bonanomi Dario D Firth Amy A Singer Oded O Trono Didier D Pfaff Samuel L SL

Nature 20120701 7405

Embryonic stem (ES) cells are derived from blastocyst-stage embryos and are thought to be functionally equivalent to the inner cell mass, which lacks the ability to produce all extraembryonic tissues. Here we identify a rare transient cell population within mouse ES and induced pluripotent stem (iPS) cell cultures that expresses high levels of transcripts found in two-cell (2C) embryos in which the blastomeres are totipotent. We genetically tagged these 2C-like ES cells and show that they lack t ...[more]

PMID: 22722858

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2C::tomato ES cells, 2-cell embryos and wild type oocytes

Project description:This SuperSeries is composed of the following subset Series: GSE33763: Expression data from 2C::tomato+ vs 2C::tomato - ES cells GSE33920: mRNA-Seq of 2C::tomato+ vs. - ES cells GSE33921: RNA-Seq from two-cell (2C) stage embryos GSE33922: RNA-Seq from wt oocytes GSE36896: RNA-Seq from wt and G9A knockout ES cells Refer to individual Series

2012-06-17 | E-GEOD-33923 | biostudies-arrayexpress

Expression data from 2C::tomato+ vs 2C::tomato - ES cells

Project description:We compared gene expression from 2C::tomato+/- ES cells from Kdm1a wt and mutant ES cultures 2C::tomato- samples 1, 5, 9 2C::tomato+ samples 2, 6, 10 We collecteded 3 replicates of RNA from 2C::tomato+ and - ES cells

2012-06-17 | E-GEOD-33763 | biostudies-arrayexpress

Expression data from 2C::tomato+ vs 2C::tomato - ES cells

Project description:We compared gene expression from 2C::tomato+/- ES cells from Kdm1a wt and mutant ES cultures 2C::tomato- samples 1, 5, 9 2C::tomato+ samples 2, 6, 10

2012-06-18 | GSE33763 | GEO

mRNA-Seq of 2C::tomato+ vs. - ES cells

Project description:We identified/quantified genes and repeat elements enriched within 2C::tomato+ cells vs. 2C::tomato - cells

2012-06-18 | GSE33920 | GEO

RNA-seq of Maternal Kdm1a mutant 2C embryos

Project description:2C embryos were generated from Kdm1a FL/Fl Zp3Cre females mated to wild type males for RNA-seq analysis using the Nugen Ovation RNA-seq system V2 3 replicates of maternal Kdm1a mutant 2C embryos were collected for RNA-seq , compared to wt 2C embryos and wt oocyte samples from Macfarlan TS et al, Nature 2012 (GEO acession GSE33923)

2015-03-10 | E-GEOD-66547 | biostudies-arrayexpress

Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E36 with H3K27ac, H3K27me1, and H3K4me1/3)

Project description:These data include the genome wide location analysis of H3K27me1/2/ac and H3K4me1/3 by ChIP in mouse ES cells. Precipitation of formaldehyde cross-linked chromatin prepared from mouse ES cell using specific antibodies against Histone H3 and its specific modifications. Rabbit IgG were used as control.

2013-12-05 | E-GEOD-39496 | biostudies-arrayexpress

Widespread Use of Non-Productive Alternative Splice Sites in Saccharomyces cerevisiae

Project description:Using RNA-Seq analysis of nonsense-mediated mRNA decay (NMD) mutant strains, we show that many Saccharomyces cerevisiae intron-containing genes exhibit usage of alternative splice sites, but most transcripts generated by splicing from these sites are non-functional because they introduce premature termination codons leading to transcript degradation by NMD. Analysis of splicing mutants combined with NMD inactivation revealed the role of specific splicing factors in governing the use of these alternative splice sites and identified novel functions for Prp17p in enhancing the use of branchpoint-proximal upstream 3M-bM-^@M-^Y splice sites and for Prp18p in suppressing the usage of a non-canonical AUG 3M-bM-^@M-^Y-splice site. The use of non-productive alternative splice sites can limit the expression of some transcripts and can be increased in stress conditions in a promoter-dependent manner, contributing to the down-regulation of genes during stress. These results reveal that alternative splicing is frequent in S.cerevisiae but masked by RNA degradation and that the use of alternative splice sites is mostly aimed at controlling transcript levels rather than increasing proteome diversity. mRNA-Seq profiling of 3 mutants in the nonsense-mediated mRNA decay pathway and wildtype yeast

2014-02-21 | E-GEOD-55213 | biostudies-arrayexpress

RNA-Seq from two-cell (2C) stage embryos

Project description:To determine gene expression in 2 cell stage embryos 3 Replicates of litters of wild type 2 cell stage embryos

2012-06-18 | E-GEOD-33921 | biostudies-arrayexpress

Yy1 occupancy of mouse ES cell genome

Project description:These data include the genome wide location analyses of Yy1 by bioChIPs of Fbio-Yy1. Streptavidin precipitation of formaldehyde cross-linked chromatin prepared from Fbio-Yy1 and control expressing mouse ES cells

2012-01-04 | E-GEOD-31785 | biostudies-arrayexpress

RNA-Seq from wt oocytes

Project description:To determine gene expression in mouse ovulated oocytes 3 Replicates of litters of wild type ovulated oocytes

2012-06-18 | E-GEOD-33922 | biostudies-arrayexpress