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

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

PROVIDER: PRJEB21275 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2004724_1.fastq.gz	Fastqsanger.gz
	ERR2004724_2.fastq.gz	Fastqsanger.gz
	ERR2004725_1.fastq.gz	Fastqsanger.gz
	ERR2004725_2.fastq.gz	Fastqsanger.gz
	ERR2004726_1.fastq.gz	Fastqsanger.gz

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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.

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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.

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

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