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STARR-seq enhancer activity in mouse embryonic stem cells cultured in 2i+LIF or serum+LIF [STARR-seq]

ABSTRACT: STARR-seq enhancer activity in mouse embryonic stem cells cultured in 2i+LIF or serum+LIF [STARR-seq]

PROVIDER: PRJNA600931 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10877354_1.fastq.gz	Fastqsanger.gz
	SRR10877354_2.fastq.gz	Fastqsanger.gz
	SRR10877355_1.fastq.gz	Fastqsanger.gz
	SRR10877355_2.fastq.gz	Fastqsanger.gz
	SRR10877356_1.fastq.gz	Fastqsanger.gz

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STARR-seq enhancer activity in mouse embryonic stem cells cultured in 2i+LIF or serum+LIF [STARR-seq]

Project description:Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells.

2020-08-16 | GSE143544 | GEO

RNA-seq analysis of ES cell populations with different functional potentials in serum/LIF and 2i/LIF, as well as analysis of the transcriptional effect of LIF in ground state (2i) culture conditions.

Project description:We report that ES cells cultured in ground state (2i and 2i/LIF) culture conditions are heterogeneous and show heterogeneus expression of extraembryonic markers. Using a highly sensitive reporter for the endoderm marker Hex we can sort Hex high and low populations from either serum/LIF or 2i/LIF and demonstrate that they have different functional properties. Here we explored the transcriptional basis of these functional differences and noted that Hex low (HV-) and Hex high (HV+) populations showed more distinct expression profiles in 2i/LIF than in serum/LIF. Additionally in 2i/LIF the HV+ population showed an upregulation of extraembryonic markers (such as trophoblast stem cell specific genes) and also imprinted genes compared to the HV- population, which is not observed when these populations are sorted from serum/LIF. We also analysed the transcriptional effect of LIF in 2i by analysing unsorted ES cells cultured in either 2i alone or 2i with LIF. We observed that the addition of LIF led to an upregulation of extraembryonic markers but did not effect the expression of pluripotency genes, other than Klf4. Additionally, the most significantly upregulated genes from 2i/LIF cultured ES cells compared to 2i cultured ES cells showed the greatest correlation to placental tissue when compared to the GNF tissue specific expression database. This analysis, alongside functional experiments, suggested that HV+ ES cells in 2i/LIF corresponded to an extraembryonically primed population of cells and that the addition of LIF supported this population.

2013-06-11 | GSE45182 | GEO

RNA-seq analysis of ES cell populations with different functional potentials in serum/LIF and 2i/LIF, as well as analysis of the transcriptional effect of LIF in ground state (2i) culture conditions.

2013-06-11 | E-GEOD-45182 | biostudies-arrayexpress

Trim24 ChIP-seq in embryonic stem (ES) cells grown by 2i+LIF (2iL) and serum media

Project description:ChIP followed by next generation sequencing against Trim24 was performed in mouse embryonic stem (ES) grown either in 2i+LIF (2iL) or serum media. Two biological replicates for each condition were sequenced using Illumina HiSeq. Two input controls (no IP) were also generated for each condition.

2016-11-08 | E-MTAB-3802 | biostudies-arrayexpress

ChIP-seq of Klf2 in mouse embryonic stem cells (Serum/LIF and 2i)

Project description:ChIP-seq of Klf2 in mouse embryonic stem cells (Serum/LIF and 2i)

| PRJEB5723 | ENA

ChIP-seq of Klf2 in mouse embryonic stem cells (Serum/LIF and 2i)

Project description:The self-renewing pluripotent state was first captured in mouse embryonic stem cells (mESCs) over two decades ago. The standard condition requires the presence of serum and LIF, which provide growth promoting signals for cell expansion. However, there are pro-differentiation signals which destabilize the undifferentiated state of mESCs. The dual inhibition (2i) of the pro-differentiation Mek/Erk and Gsk3/Tcf3 pathways in mESCs is sufficient to establish an enhanced pluripotent “ground state” which bears features resembling the pre-implantation mouse epiblast. Gsk3 inhibition alleviates the repression of Esrrb, a transcription factor that can substitute for Nanog function in mESCs. The molecular mechanism that is mediated by Mek inhibition is however not clear. In this study, we investigate the pathway through which Mek inhibition operates to maintain ground state pluripotency. We have found that in mESCs, Kruppel-like factor 2 (Klf2) is a protein target of the Mek/Erk pathway; and that Klf2 protein is phosphorylated by Erk2 and subsequently degraded through the proteosome. It is therefore by Mek-inhibition through PD0325901 or 2i that enables the stabilization and accumulation of Klf2 to sustain ground state pluripotency. Importantly, we found that Klf2-null mESCs, while viable under LIF/Serum conditions, cannot be maintained and eventually gradually die within a few passages. Our result thus demonstrates that Klf2 is an essential factor of ground state pluripotency. Collectively, our study defines the Mek/Klf2 axis that cooperates with the Gsk3/Esrrb pathway in mediating ground state pluripotency.

2014-06-04 | E-MTAB-2365 | biostudies-arrayexpress

Distinct DNA methylomes of 2i and serum mouse ES cells are interconvertible and reflect pre- and post-implantation embryonic states

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

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [single_cell_RNA-Seq]

2020-08-16 | GSE143545 | GEO

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [RNA-Seq]

2020-08-16 | GSE143543 | GEO

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [ChIP-seq]

2020-08-16 | GSE143541 | GEO