Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA130405 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study describes the DNA methylation profiling using whole-genome bisulfite sequencing of mouse ES cells, either derived and maintained in 2i serum-free NDiff medium, or in the presence of serum and LIF, or maintained and derived in the presence of serum and LIF and subsequently adapted to 2i serum-free NDiff medium, or maintained and derived in the presence of 2i and LIF and subsequently adapted to 2i serum. DNA methylation profiling using whole-genome bisulfite sequencing of 14 samples, 3 different lines (E14, XT67E1, Rex/GFP-2i) of pluripotent mouse ES cells as well during conversion from 2i to serum and vice versa.
2013-07-12 | E-GEOD-41923 | biostudies-arrayexpress
Project description:This study describes the DNA methylation profiling using whole-genome bisulfite sequencing of mouse ES cells, either derived and maintained in 2i serum-free NDiff medium, or in the presence of serum and LIF, or maintained and derived in the presence of serum and LIF and subsequently adapted to 2i serum-free NDiff medium, or maintained and derived in the presence of 2i and LIF and subsequently adapted to 2i serum.
2013-07-12 | GSE41923 | GEO
Project description:The pluripotent ground state is defined as a basal state free of epigenetic restrictions, which influence lineage specification. While naive embryonic stem cells (ESCs) can be maintained in a hypomethylated state with open chromatin when grown using two small-molecule inhibitors (2i)/leukemia inhibitory factor (LIF), in contrast to serum/LIF-grown ESCs that resemble early post-implantation embryos, broader features of the ground-state pluripotent epigenome are not well understood. We identified epigenetic features of mouse ESCs cultured using 2i/LIF or serum/LIF by proteomic profiling of chromatin-associated complexes and histone modifications. Polycomb-repressive complex 2 (PRC2) and its product H3K27me3 are highly abundant in 2i/LIF ESCs, and H3K27me3 is distributed genome-wide in a CpG-dependent fashion. Consistently, PRC2-deficient ESCs showed increased DNA methylation at sites normally occupied by H3K27me3 and increased H4 acetylation. Inhibiting DNA methylation in PRC2-deficient ESCs did not affect their viability or transcriptome. Our findings suggest a unique H3K27me3 configuration protects naive ESCs from lineage priming, and they reveal widespread epigenetic crosstalk in ground-state pluripotency.
2018-11-24 | GSE101675 | GEO
Project description:Pluripotent mouse embryonic stem cells (ESCs) were originally derived and stably maintained on feeder cells such as inactivated mouse embryo fibroblasts, and can generate complete ESC-pups by tetraploid embryo complementation (TEC), the most stringent functional test of naive pluripotency. Remarkably, 2i (inhibitors of Mek and Gsk3β signaling) medium with LIF in the absence of serum and feeders was developed to achieve ground state of mouse ESCs, and also has been successfully used for derivation of germline competent ESCs in other species such as rat. Notably, 2i-culture gives rise to transcriptional profiles and epigenetic landscapes quite distinct from serum-based ESCs. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of ESCs cultured in four different conditions: serum without feeder, serum with feeder, serum with feeder and 2i, and N2B27+2i.
2018-01-20 | GSE109418 | GEO
Project description:Mouse embryonic stem (ES) cells are locked into self-renewal by shielding from inductive cues. Release from this ground state in minimal conditions offers a system for delineating developmental progression from naive pluripotency. Here we examined the initial transition process. The ES cell population behaves asynchronously. We therefore exploited a short-half-life Rex1::GFP reporter to isolate cells either side of exit from naive status. Differentiation of Rex1-GFPd2 ES cells was initiated by withdrawing 2i (Kalkan et al., 2016). Undifferentiated 2i-cells and post-2i withdrawal differentiating populations (16h, 25h-Rex1-High, 25h-Rex1-Low) were subjected to proteomic analysis by Mass Spectrometry.
2017-02-22 | PXD005581 | Pride
Project description:The ground state of pluripotency is defined as a minimal unrestricted state as present in the Inner Cell Mass (ICM). Mouse embryonic stem cells (ESCs) grown in a defined serum-free medium with two kinase inhibitors (‘2i’) reflect this state, whereas ESCs grown in the presence of serum (‘serum’) share more similarities with post implantation epiblast cells. Pluripotency results from an intricate interplay between cytoplasmic, nuclear and chromatin-associated proteins. Therefore, quantitative information on the (sub)cellular proteome is essential to gain insight in the molecular mechanisms driving different pluripotent states. Here, we describe a full SILAC workflow and quality controls for proteomic comparison of 2i and serum ESCs. We demonstrate that this workflow is applicable for subcellular proteomics of the cytoplasm, nuclear and chromatin. The obtained quantitative information revealed increased levels of naïve pluripotency factors on the chromatin of 2i ESCs. Further, we demonstrate that these pluripotent states are supported by distinct metabolic programs, which include upregulation of free radical buffering by the glutathione pathway in 2i ESCs. Through induction of intracellular radicals, we show that the altered metabolic environment renders 2i ESCs less sensitive to oxidative stress. Altogether, this work provides novel insights into the proteome landscape underlying ground state pluripotency.
2018-11-07 | PXD009217 | Pride
Project description:This study describes the epigenetic and transcriptome profiling of mouse ES cells cultures in 2i serum-free medium. The proteins for which ChIP-Seq profiles were generated in these cells, as well as for cells grown in serum conditions, include H3K4me3, H3K36me3, H3K27me3, H3K9me3, Suz12 and Ezh2. A sequence profile of genomic DNA is also included. Furthermore, we included RNA-Seq of ds_cDNA synthesized from double poly(A) selected mRNA and from rRNA depleted (strand specific) total RNA. ChIP-Seq profiling and RNA-Seq profiling on mouse naive ES cells
2012-04-26 | E-GEOD-23943 | biostudies-arrayexpress
Project description:ChIP-seq to map the binding sites for CTCF and cohesin subunit Rad21 in the naive mES cells (46C cell line grown in the 2i/LIF condition) and in the neural stem cells (derived from the 46C ES cells using the mono-layer differentiation protocol, grown in the N2B27 medium these cells are Nestin+). The naive mES cells were grown in two different media (fetal bovine serum, FBS and 2i/LIF culture - naive pluripotency conditions) as detailed in the growth protocols.
2018-11-08 | E-MTAB-5732 | biostudies-arrayexpress
Project description:Identification of transcripts in murine embryonic stem (ES) cell lines growing under 3 different self-renewing conditions; GMEM + 10% FCS, N2B27 + 2i (1 μM PD032 and 3 μM CHIR99021) and knockout serum replacement (KOSR) medium (80% Knockout DMEM, 20% Knockout Serum Replacement). Under all conditions, ES cells were grown on gelatin-coated dishes and passaged by trypsinisation. ES cells were cultured in each condition for at least 3 passages prior to sample collection. The aim of this array experiment is to identify significant differences in transcript levels of ES cells grown under different conditions. Differences of transcript levels from the different conditions should be consistent among the biological and technical replicates for each.
2016-07-14 | GSE72445 | GEO
Project description:These are 3 TMT10 samples. The indicated "standard" sub-samples all refer to the same biological sample (obtained as a mixture of all other samples), split and tagged as indicated, to play as a reference for normalization.
TMT10 sample1 contains the following sub-samples:
-TAG 126: Standard.
-TAG 127N: Day 3 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 127C: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 128N: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 128C: Not relevant.
-TAG 129N: Not relevant.
-TAG 129C: Not relevant.
-TAG 130N: Not relevant.
-TAG 130C: RSet medium.
-TAG 131: Standard.
TMT10 sample2 contains the following sub-samples:
-TAG 126: Standard
-TAG 127N: Day 3 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 127C: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 128N: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 128C: Not relevant.
-TAG 129N: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 129C: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 130N: Not relevant.
-TAG 130C: RSet medium.
-TAG 131: Standard.
TMT10 sample3 contains the following sub-samples:
-TAG 126: Standard.
-TAG 127N: Day 3 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 127C: Day 3 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 128N: Day 2 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 128C: Day 2 conditioned medium of replication-incompetent MEFs cultured on VTN coating in RSeT medium.
-TAG 129N: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a MEF feeder-layer in RSeT medium.
-TAG 129C: Day 2 conditioned medium of naive human pluripotent stem cells cultured on a VTN coating in RSeT medium.
-TAG 130N: Not relevant.
-TAG 130C: RSet medium.
-TAG 131: Standard.
Detailed culture and processing methods are described in Cesare et al, under submission.
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