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E-MTAB-9194

ABSTRACT: RNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

PROVIDER: E-MTAB-9194 | ExpressionAtlas | 2025-01-16

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-9194-analysis-methods.tsv	Tabular
	E-MTAB-9194-analytics.tsv	Tabular
	E-MTAB-9194-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-9194-configuration.xml	Xml
	E-MTAB-9194-g2_g3-mvaPlot.png	Other

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RNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

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Cell cycle states of pluripotent cells dictate lineage decisions

Project description:Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling, to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying a retinoic acid-based differentiation protocol we show that only cells in the G2/M phase are capable of differentiating into extraembryonic endoderm cells (XENs), whereas cells in the G1 phase predominantly produce epiblast stem cells (EpiSCs). Mechanistically, we show that Esrrb is a potent XEN state inducer as it is predominantly upregulated during G2/M phase, and cells engineered to overexpress Esrrb during G1 phase forced the cells to become XENs. Interestingly, this phenomenon is unique to the pluripotency ground state as sorting cells after 48 hours of differentiation resulted in a cell cycle-independent differentiation decisions. Cells in both G1 and G2/M phases contributed equally to EpiSC and XEN cellular lineages. Taken together, this study reveals an important functional link between cell-cycle states of pluripotent cells and lineage decisions, emphasizing the regulatory role of cell cycle during exit from pluripotency and can be further expand our understanding of early differentiation events.

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E-MTAB-5219

Project description:Global expression profiling time series of early human embryonic stem cell differentiation towards the mesoderm lineage

2025-01-23 | E-MTAB-5219 | ExpressionAtlas

RNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to investigate transcriptional dynamics during definitive endoderm differentiation of human embryonic stem cells (hESCs) in early G1 phase of the cell cycle. For this, the FUCCI system was used to sort hESCs in Early G1 (EG1). Samples were taken at 0h (hESCs), 12h, 24h, 36h, 48h, 60h and 72h in triplicates. Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) and residual genomic DNA was removed using the On-Column DNase I Digestion Set (Sigma-Aldrich) following manufacturer’s instructions. The libraries were generated at a library fragment size between 100 bp to 1 kb with Stranded RNAseq Standard with Oligo dT pulldown. All samples were amplified with a standard 10 PCR cycle before sequencing. The samples were multiplexed and analysed by Illumina Hiseq V4 with a paired end read-length PE75. RNA-seq data analysis was performed following recommendations described in Conesa et al. (DOI https://doi.org/10.1186/s13059-016-0881-8).

2020-09-07 | E-MTAB-9194 | biostudies-arrayexpress

ChIP-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to investigate histone modification changes during cell cycle progression of human embryonic stem cells (hESCs) during definitive endoderm differentiation. For this, FUCCI hESCs were sorted in Early G1 (EG1), and differentiation into endoderm was performed for up to 72 hours with a combination of cytokines as described in Pauklin and Vallier (2013) and Pauklin et al. (2016). ChIP-seq was generated at 12-hour and 36-hour time-points for H3K4me3, H3K27ac, H3K4me1, H3K36me3 and H3K27me3. Library preparation and sequencing were performed at the Wellcome Sanger Institute next-generation sequencing facility on Illumina HiSeq 2000, 2 x 75bp paired-end reads. ChIP-seq data from other time-points (0h, 24h, 48h and 72h) of the same experimental set-up is available elsewhere (GEO DataSet, accession PRJNA593217). All processed ChIP-seq data is publicly available at http://ngs.sanger.ac.uk/production/endoderm

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ATAC-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to look into chromatin accessibility changes during cell cycle progression in human embryonic stem cells (hESCs) during definitive endoderm differentiation. For this, FUCCI hESCs were sorted in Early G1 (EG1), and differentiation into endoderm was performed for up to 72 hours with a combination of cytokines as described in Pauklin and Vallier (2013) and Pauklin et al. (2016). Samples at 0, 12, 24, 36, 48 and 72 hours were generated from two independent experiments, with 100,000 cells per sample, as previously described in Kumasaka et al. (2016). Library preparation and sequencing were performed at the Wellcome Sanger Institute next-generation sequencing facility. ATAC-seq libraries were prepared with one of i5 and i7 Nextera tags combination (see protocol details), and pooled equimolarly. Sequencing was performed on Illumina HiSeq 2000, 2 x 75bp paired-end reads.

2020-09-07 | E-MTAB-9124 | biostudies-arrayexpress

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