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Decoding the Universal Human Chromatin Landscape through Teratoma-Based Profiling [ChIP-seq]

ABSTRACT: Decoding the Universal Human Chromatin Landscape through Teratoma-Based Profiling [ChIP-seq]

PROVIDER: PRJNA955710 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24172900_1.fastq.gz	Fastqsanger.gz
	SRR24172900_2.fastq.gz	Fastqsanger.gz
	SRR24172901_1.fastq.gz	Fastqsanger.gz
	SRR24172901_2.fastq.gz	Fastqsanger.gz
	SRR24172902_1.fastq.gz	Fastqsanger.gz

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Decoding the Universal Human Chromatin Landscape through Teratoma-Based Profiling

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Project description:Teratoma formation is key for evaluating differentiation of human pluripotent stem cells into embryonic germ layers and serves as a model for understanding stem cell differentiation and developmental processes. Its potential for insights into epigenome and transcriptome profiling is significant. This study integrates the analysis of the epigenome and transcriptome of hESC-generated teratomas, comparing transcriptomes between hESCs and teratomas. It employs cell type-specific expression patterns from single-cell data to deconvolve RNA-Seq data and identify cell types within teratomas. Our results provide a catalog of activating and repressive histone modifications, while also elucidating distinctive features of chromatin states. Construction of an epigenetic signature matrix enabled the quantification of diverse cell populations in teratomas and enhanced the ability to unravel the epigenetic landscape in heterogeneous tissue contexts. This study also includes a single cell multiome atlas of expression (scRNA-Seq) and chromatin accessibility (scATAC-Seq) of human teratomas, further revealing the complexity of these tissues. A histology-based digital staining tool further complemented the annotation of cell types in teratomas, enhancing our understanding of their cellular composition. This research is a valuable resource for examining teratoma epigenomic and transcriptomic landscapes and serves as a model for epigenetic data comparison.

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Decoding the Universal Human Chromatin Landscape through Teratoma-Based Profiling [RNA-seq]

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Decoding the Universal Human Chromatin Landscape through Teratoma-Based Profiling [ChIP-seq]

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Decoding the universal human chromatin landscape through teratoma-based profiling.

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Decoding the Universal Human Chromatin Landscape through Teratoma-Based Profiling

Project description:This SuperSeries is composed of the SubSeries listed below.

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Identification of new (liquid) biomarkers for teratoma in general and the growing teratoma syndrome

Project description:In germ cell tumors (GCT), a growing mature teratoma during or after chemotherapy with decreasing tumor markers is defined as ´growing teratoma syndrome` (GTS) according to its first describer Logothetis et al. in 1982. Due to the small number of available cases worldwide, not much is known about this continuously growing tumor and its pathogenesis. Especially in cases with extensive and surgical uncontrollable tumor mass, specific therapeutic options and biomarkers early indicating presence of GTS are still lacking. In this study, GTS was stratified into a slow (< 0.5 cm / month), medium (0.5 – 1.5 cm / month) and rapid (> 1.5 cm / month) group based on the tumor growth rate. We analyzed the secretome of 3 GTS samples of each subgroup and 3 teratomas. The secreted proteins were isolated from ex vivo cultivated tissues and analyzed by liquid-chromatography coupled to mass spectrometry (LS-MS).

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