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Single nuclear RNA sequencing and 10X spatial transcriptomic profiling of murine tumors initiated by transplantation of engineered prostate organoids [snRNA-seq]

ABSTRACT: Single nuclear RNA sequencing and 10X spatial transcriptomic profiling of murine tumors initiated by transplantation of engineered prostate organoids [snRNA-seq]

PROVIDER: PRJNA1034583 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26630500_1.fastq.gz	Fastqsanger.gz
	SRR26630500_2.fastq.gz	Fastqsanger.gz
	SRR26630501_1.fastq.gz	Fastqsanger.gz
	SRR26630501_2.fastq.gz	Fastqsanger.gz
	SRR26630499_1.fastq.gz	Fastqsanger.gz

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Profiling of murine tumors initiated by transplantation of engineered prostate organoids

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Single nuclear RNA sequencing and 10X spatial transcriptomic profiling of murine tumors initiated by transplantation of engineered prostate organoids [snRNA-seq]

Project description:Single-nuclear RNA-sequencing of murine organoid transplant-derived prostate tumors. Purpose: To identify differences in cell composition in murine prostatic tumors and to generate a reference dataset of all major cell types present in mouse prostate tumors Results: We recovered 4,872 cells with a median of 7055.5 UMIs per cell. Conclusions: snRNASeq reveals heterogeneity within neuroendocrine prostate cancer compartment, dominated by an Ascl1+ expression profile with mixed luminal lineage marker genes. snRNASeq recovers all the major epithelial, immune, and stromal cell types in prostate tumors. Spatial transcriptomic profiling of murine prostate tumors. Purpose: To spatially map the major cell types in the mouse prostatic tumors and identify spatially distinct neuroendocrine tumor compartments. Distinct tumor microenvironments were also used for identification of cell:cell signaling axes distributed between the histological subtypes. Conclusions: Spatial transcriptomic profiling of the mouse prostate reveals all major cell types and allows for cell:cell signaling analyses upon integration with our matching snRNA-Seq data

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snRNA-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snRNA-seq data is uploaded here.

2025-04-22 | E-MTAB-13651 | biostudies-arrayexpress

Single nuclear RNA sequencing and 10X spatial transcriptomic profiling of murine tumors initiated by transplantation of engineered prostate organoids [visium]

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snRNA-seq of whole hearts from adult BL6 mice

Project description:We used snRNA-seq to investigate an entire adult mammalian heart of BL6 mice. Whole hearts were harvested from 4 male mice (12 weeks) after cervical dislocation. The hearts were pooled and nuclei isolated using the Nuclei PURE Prep isolation kit (Sigma-Aldrich, Darmstadt, Germany) according to the manufacturer’s protocol. Sequencing was conducted by Genewiz (Leipzig, Germany) on the 10xGenomics system. Single nuclei were captured in droplet emulsions and snRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3′ Gel Bead and Library V3 Kit. RNA was controlled for sufficient quality on an Agilent 2100 Bioanalyzer system and quantified using a Qubit Fluorometer.

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snATAC-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

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Project description:snRNA on human pancreas. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR496XXB). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

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