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Mouse embryonic stem cells LCMS-MS

ABSTRACT: We hypothesized that uncovering interactions between Pfkp and other proteins could help resolve the mechanism whereby Pfkp regulates germ layer differentiation. Towards this, Pfkp was immunoprecipitated from mESCs and mass spectrometry analysis used to identify a number of potential Pfkp-interacting proteins

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture, Embryonic Stem Cell

DISEASE(S): Disease Free

SUBMITTER: ruijie wang

LAB HEAD: Mian Wu

PROVIDER: PXD038944 | Pride | 2023-02-23

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	WRJ_F.mgf	Mgf
	WRJ_F.msf	Msf
	WRJ_F.raw	Raw
	WRJ_P.mgf	Mgf
	WRJ_P.msf	Msf

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1 - 5 of 7

Publications

Glycolytic Pfkp acts as a Lin41 protein kinase to promote endodermal differentiation of embryonic stem cells.

Cao Leixi L Wang Ruijie R Liu Guangzhi G Zhang Yuwei Y Thorne Rick Francis RF Zhang Xu Dong XD Li Jinming J Xia Yang Y Guo Lili L Shao Fengmin F Gu Hao H Wu Mian M

EMBO reports 20230120 3

Unveiling the principles governing embryonic stem cell (ESC) differentiation into specific lineages is critical for understanding embryonic development and for stem cell applications in regenerative medicine. Here, we establish an intersection between LIF-Stat3 signaling that is essential for maintaining murine (m) ESCs pluripotency, and the glycolytic enzyme, the platelet isoform of phosphofructokinase (Pfkp). In the pluripotent state, Stat3 transcriptionally suppresses Pfkp in mESCs while mani ...[more]

PMID: 36660859

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Changes in replisome composition underlie the rewiring of DNA replication during embryonic stem cell reprogramming

Project description:Pluripotent stem cells can give rise to the three embryonic germ layers and the characterization of their properties is crucial to exploit their therapeutic potential. Mouse embryonic stem cells (mESCs) are isolated and usually maintained in vitro in a primed state that resembles the post-implantation epiblast features. Furthermore, primed mESCs can be de-differentiated to a naive state that resembles the pre-implantation inner cell mass (ICM). Cell differentiation or genotoxic stress, among others, can alter DNA replication, which is a flexible process able to adapt to different cellular contexts. Here, we demonstrate that primed-to-naive mESC reprogramming triggers replication fork slowdown, increased fork asymmetry and a compensatory activation of dormant origins. Using iPOND (“isolation of proteins on nascent DNA”) coupled to mass spectrometry we have characterized the changes in replisome composition between naive and primed mESCs. Several DNA repair factors, including MRE11 nuclease, are enriched in naive mESCs forks, while factors involved in ubiquitin-dependent protein metabolism are enriched in primed mESC forks. We report that primed-to-naive mESC de-differentiation promotes recruitment of MRE11 to the forks in response to transcription-replication conflicts, underlying the DNA replication rewiring required for efficient mESC reprogramming.

2024-04-03 | PXD041946 | Pride

Small RNA profiling of WT E14, Ago2_KO and Ago1_KO mouse embryonic stem cells before and after XEN conversion and small RNA profiling after Immunoprecipitation of AGO1&2 proteins in WT E14, Ago1_KO and Ago2_KO mESCs.

Project description:Purpose: The goals of this study was to obtain the profile total miRNAs in WT E14, Ago2_KO and Ago1_KO mESCs to compare it with Immunoprecipitated microRNAs in AGO1&2 proteins.

2018-02-02 | GSE80211 | GEO

Comparison of transcriptional profiles between naive, primed and ground state pluripotency in mouse embryonic stem cells of the same genetic background

Project description:Derivation of naive state of mouse embryonic stem cells (mESCs) in LIF+serum (LS) culture condition is strain dependent, whereas derivation of ground state mESCs is readily possible from all strains tested so far in “2i” culture condition. ESCs can be derived from the post-implantation stage mouse embryos (EpiSCs), showing primed characteristics. In the present study, we characterized and compared the transcriptional profile of naïve, primed and ground state mESCs. Considering the importance of genetic background of mouse model for ESCs derivation in conventional culture conditions, all ESCs lines used in the study were derived from the same strain of mice. We found distinct transcriptional profiles between naive, primed and ground state mESCs. Primed state mESCs exhibit lower expression of pluripotency markers along with higher expression of lineage specific markers compared to naive and ground state mESCs. We also demonstrate that the differentiation propensity of ESCs to specific germ layer varies depending on the pluripotency state of ESCs.

2018-04-12 | GSE78144 | GEO

Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO ChIP-Seq)

Project description:During mammalian development DNA methylation patterns need to be reset in primordial germ cells (PGC) and preimplantation embryos. However, many retro-transposons and imprinted genes are resistant to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that some of these sequences are immune to widespread erasure of DNA methylation in the mouse embryonic stem cells (mESCs) lacking de novo DNA methyltransferases. Persistence of DNA methylation at these loci in mESCs depends on the histone H3K9 methyltransferase Setdb1, as deletion of Setdb1 results in reduction of H3K9me3 and DNA methylation levels concomitant with an increase in 5-hydroxymethylation (5hmC). In addition, depletion of H3K9 methyltransferase G9a leads to genome-wide reduction of DNA methylation but to a lesser extent at the above sequences. Taken together, these data reveal that Setdb1 ensures the fidelity of DNA methylation at specific loci in mESCs, which may reflect mechanisms functioning in vivo during key developmental stages. Examination of H3K9me3 histone modifications in 2 cell types.

2014-06-03 | E-GEOD-47878 | biostudies-arrayexpress

Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO RNA-Seq)

2014-06-03 | E-GEOD-47883 | biostudies-arrayexpress

Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO Methyl-Seq)

2014-06-03 | E-GEOD-47890 | biostudies-arrayexpress

Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO Methyl-Seq)

2014-06-03 | E-GEOD-47893 | biostudies-arrayexpress

Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO ChIP-Seq)

2014-06-03 | E-GEOD-47887 | biostudies-arrayexpress

Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO 5hmC-capture-seq)

2014-06-03 | E-GEOD-47892 | biostudies-arrayexpress

An ERK5-KLF2 signalling module regulates early embryonic gene expression dynamics and stem cell rejuvenation

Project description:CCE mESCs were transfected with either empty pCAGGS vector or HA-MEK5DD (S311D T315D) construct for 48 hours. 24 hours prior to lysis, mESCs were either treated with 10uM AX15836 or DMSO control, and transfected mESCs selected with puromycin. Conditions were performed in triplicate.

2021-03-18 | PXD024679 | Pride

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