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Genome-wide maps of chromatin state in cultured male germline stem cells [scATAC-seq]

ABSTRACT: Genome-wide maps of chromatin state in cultured male germline stem cells [scATAC-seq]

PROVIDER: PRJNA668908 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12817011_1.fastq.gz	Fastqsanger.gz
	SRR12817011_2.fastq.gz	Fastqsanger.gz
	SRR12817012_1.fastq.gz	Fastqsanger.gz
	SRR12817012_2.fastq.gz	Fastqsanger.gz
	SRR12817013_1.fastq.gz	Fastqsanger.gz

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Genome-wide maps of chromatin state in cultured male germline stem cells with retinoic acid treatment [scATAC-seq]

Project description:Genome-wide maps of chromatin state in cultured male germline stem cells with retinoic acid treatment [scATAC-seq]

| PRJNA704903 | ENA

Genome-wide maps of chromatin state in cultured male germline stem cells [scATAC-seq]

Project description:We report the application of single-cell ATAC-seq to reconstruct the epigenetic program and identify key transcription factors and cis-regulatory elements associated with the epithelial and mesenchymal heterogeneity and G9a inhibition in cultured male germline stem cells (GSCs). First, we identified epithelial-like and mesenchymal-like clusters in the sample. Pseudotime trajectory also indicated that GSCs could undergo EMT-like process with unique regulators in different stages. Lastly, we showed that G9a inhibition could suppress the EMT-like process in GSCs.

2023-07-01 | GSE159414 | GEO

Genome-wide maps of chromatin state in cultured male germline stem cells with retinoic acid treatment [scATAC-seq]

Project description:We report the application of single-cell ATAC-seq to reconstruct the epigenetic program and differentiation trajectory associated with the retinoic acid (RA)-induced differentiation in cultured male germline stem cells (GSCs). We also identified key transcription factors and regulatory elements regulated by RA.

2022-12-21 | GSE167531 | GEO

scATAC-Seq reveals heterogeneity associated with spermatogonial differentiation in cultured male germline stem cells.

Project description:Spermatogonial stem cells are the most primitive spermatogonia in testis, which can self-renew to maintain the stem cell pool or differentiate to give rise to germ cells including haploid spermatids. All-trans-retinoic acid (RA), a bioactive metabolite of vitamin A, plays a fundamental role in initiating spermatogonial differentiation. In this study, single-cell ATAC-seq (scATAC-seq) was used to obtain genome-wide chromatin maps of cultured germline stem cells (GSCs) that were in control and RA-induced differentiation states. We showed that different subsets of GSCs can be distinguished based on chromatin accessibility of self-renewal and differentiation signature genes. Importantly, both progenitors and a subset of stem cells are able to respond to RA and give rise to differentiating cell subsets with distinct chromatin accessibility profiles. In this study, we identified regulatory regions that undergo chromatin remodeling and are associated with the retinoic signaling pathway. Moreover, we reconstructed the differentiation trajectory and identified novel transcription factor candidates enriched in different spermatogonia subsets. Collectively, our work provides a valuable resource for understanding the heterogeneity associated with differentiation and RA response in GSCs.

| S-EPMC9744833 | biostudies-literature

Genome-wide maps of chromatin state in mouse perinatal testes [scATAC-seq]

Project description:Genome-wide maps of chromatin state in mouse perinatal testes [scATAC-seq]

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Genome-wide maps of chromatin state for LAG-1 in germline

Project description:Genome-wide maps of chromatin state for LAG-1 in germline

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Genome-wide maps of chromatin state in mouse perinatal testes [scATAC-seq]

Project description:We report the application of single-cell ATAC-seq to reconstruct the epigenetic program and identify key transcription factors and cis-regulatory elements during the perinatal testiscular develpment. First, we constructed sequencing libraries from testes collected from E18.5, PND0, PND3 and PND6 mice. The cell clusters identidied from scATAC-seq were assigned to known testicular cell types, including germ cells, Sertoli cells, Leydig cells, peritubular myoid cells, stromal cells, endothelial cells and blood cells. We then constructed pseudotime developmental trajectories and identified transcription factor regulators for each cell type. Lastly, we identified cis-regulatory elements such peak-to-gene linkages across testis.

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Genome-wide maps of chromatin state for LAG-1 in germline

Project description:We report the application of conventional ChIP-seq analysis for LAG-1 chromatin state in germline. We identified 137 genes putatively regulated by LAG-1 that's overlapped by three independent biological replicates. These genes included previously known targets lst-1, sygl-1, and mir-61/250.

2020-02-17 | GSE144223 | GEO

Single-cell chromatin accessibility data using scATAC-seq

Project description:Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.

2015-06-17 | E-GEOD-65360 | biostudies-arrayexpress

Gene expression and chromatin accessibility profiles of cultured male germline stem cells [RNA-seq and ATAC-seq]

Project description:We report the application of RNA-seq to profile the transcriptome associated with Oct4-GFP intensity, feeder v.s. feeder-free culture, epithelial and mesenchymal heterogeneity and G9a inhibition in cultured male germline stem cells (GSCs). First, we confirmed that the self-renewal gene expression levels of feeder culture and feeder-free culture were comparable to each other. Next, we investigatied the transcriptional differences among GSCs with different Oct4-GFP intensity. Then, we explored the transcriptonal differences between epithelial-like and mesenchymal-like GSCs, demonstrating GSCs could undergo an EMT-like process. Lastly, we showed that G9a inhibition could suppress the EMT-like process in GSCs.

2023-07-01 | GSE159412 | GEO

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