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ATAC-seq of human embryonic stem cells during cell cycle progression

ABSTRACT: ATAC-seq of human embryonic stem cells during cell cycle progression

PROVIDER: PRJEB34481 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3528822_1.fastq.gz	Fastqsanger.gz
	ERR3528822_2.fastq.gz	Fastqsanger.gz
	ERR3528823_1.fastq.gz	Fastqsanger.gz
	ERR3528823_2.fastq.gz	Fastqsanger.gz
	ERR3528824_1.fastq.gz	Fastqsanger.gz

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ATAC-seq of human embryonic stem cells during cell cycle progression

Project description:The experiment was designed to look into chromatin accessibility changes during cell cycle progression in human embryonic stem cells (hESCs). For this, FUCCI hESCs are sorted in Early G1 (EG1), Late G1 (LG1), G1/S transition and S/G2/M phases in duplicates. 100,000 were used per sample, as described in 2.4. Library preparation and sequencing were performed at the Wellcome Trust Sanger Institute next-generation sequencing facility. 8 ATAC-seq libraries were prepared with one of i5 and i7 Nextera tags combination (see 2.4), and pooled equimolarly. Sequencing was performed on Illumina HiSeq 2000, 2 X 75bp paired-end reads obtaining more than 60M mapped reads per library.

2023-06-24 | E-MTAB-8348 | biostudies-arrayexpress

RNA-seq of human embryonic stem cells during cell cycle progression

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ChIP-seq of human embryonic stem cells during cell cycle progression

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RNA-seq of human embryonic stem cells during cell cycle progression

Project description:The experiment was designed to look into transcriptional changes during cell cycle progression in human embryonic stem cells (hESCs). For this, FUCCI hESCs are sorted in Early G1 (EG1), Late G1 (LG1), and S/G2/M phases in triplicates, RNA was extracted and PolyA purified libraries were generated and sequenced in one HIGH Output NextSeq run Cycle, 2 X 75bp, paired-end reads.

2023-06-24 | E-MTAB-8347 | biostudies-arrayexpress

Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.

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ChIP-seq of human embryonic stem cells during cell cycle progression

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