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

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

PROVIDER: PRJEB10107 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR976966.fastq.gz	Fastqsanger.gz
	ERR976967.fastq.gz	Fastqsanger.gz
	ERR976968.fastq.gz	Fastqsanger.gz
	ERR976969.fastq.gz	Fastqsanger.gz
	ERR976970.fastq.gz	Fastqsanger.gz

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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

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

Genome-wide transcriptome analysis of pluripotent (2iL or 2i) and differentiated mES cells

Project description:We report the application of genome-wide RNA-sequencing analysis for pluripotent mouse ES cells maintained in 2iL or 2i and differentiated for 12, 24, 36, 48, 60, 72, 84, 96 hours. We find that cells differentiating from both 2iL and 2i follow a similar trajectory with 2i samples accelerated by 24 hours. Moreover we performed unsupervised hierarchical clustering on cells differentiating from 2iL and defined 6 groups of genes (gene signatures) based on their transcriptional behaviour during differentiation. Finally we reported that only after activation and dissolution of the formative signatures cells are fully committed. The same behaviour is true for cells differentiating from 2i.

2023-01-25 | GSE184134 | GEO

Trim24 knock down in the 2i-state of the mouse ES cells

Project description:Differentially expressed genes were determined by single-end sequencing (stranded protocol) following Trim24 and/or p53 knock down in the mouse ES cells grown in 2i media. Triplicates were generated for treatment and control samples but for p53 knock down (duplicate).

2017-11-08 | E-MTAB-4893 | biostudies-arrayexpress

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.

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

Genome-wide analysis of gene expression in LIF and LIF plus 2I in C57BL/6 mouse embryonic stem cells (B6 mESCs)

Project description:Analysis of genes induced by 2I condition 2i contains glycogen synthase kinase 3 (GSK3) and mitogen-activated protein kinase kinase (MEK) inhibitors: 3uM Chir99021 and 1uM PD0325901 Total RNA obtained from B6 mESCs treated with LIF or LIF/2I for 12 hours.

2013-04-26 | E-GEOD-46369 | biostudies-arrayexpress

RNA-seq on Hesx1+/+ and Hesx1-/- ES cells deprived of 2i/LIF for 24 hours

Project description:Hesx1+/+ and Hesx1-/- ES cells were cultured in 2i/LIF conditions for 5 passages, to induce a ground pluripotency state. Subsequently, inhibitors were removed to stimulate exit from ground pluripotency, and whole transcriptomics analysis was performed 24 hours after removal.

2018-05-21 | E-MTAB-5816 | biostudies-arrayexpress

Trim24 knock down in the 2i-state of the mouse ES cells

Project description:Trim24 knock down in the 2i-state of the mouse ES cells

| PRJEB14679 | ENA

Trim24 knock down in the 2i-state of the mouse ES cells

Project description:Trim24 knock down in the 2i-state of the mouse ES cells

| PRJEB17955 | ENA