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Multiome analysis (ATAC + Gene Expression (GEX)) of SUN1 knockout and control CT26 tumors grown in syngeneic mouse model

ABSTRACT: Multiome analysis (ATAC + Gene Expression (GEX)) of SUN1 knockout and control CT26 tumors grown in syngeneic mouse model

PROVIDER: PRJNA1090868 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28422194_1.fastq.gz	Fastqsanger.gz
	SRR28422194_2.fastq.gz	Fastqsanger.gz
	SRR28422195_1.fastq.gz	Fastqsanger.gz
	SRR28422195_2.fastq.gz	Fastqsanger.gz
	SRR28422196_1.fastq.gz	Fastqsanger.gz

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Multiome analysis (ATAC + Gene Expression (GEX)) of SUN1 knockout and control CT26 tumors grown in syngeneic mouse model

Project description:T cell infiltration is essential for immune checkpoint inhibitors to be effective in treating solid cancers. Through a bioinformatic pipeline, we identified a target gene SUN1 that might relate to modulating immune cell infiltration and immune response. Thus, we generated one Sun1_knockout CT26 cell line (Sun1_KO) using CRISPR-Cas9. By performing multiome single nuclei sequencing using tumors grown in syngeneic model, we set out to understand how mouse Sun1 can affect the regulatory network in tumor cells in vivo.

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RNA-Seq analysis of SUN1 knockout and control CT26 cells and tumors

Project description:T cell infiltration is essential for immune checkpoint inhibitors to be effective in treating solid cancers. Through a bioinformatic pipeline, we identified a target gene SUN1 that might relate to modulating immune cell infiltration and immune response. Thus, we generated one Sun1_knockout CT26 cell line (Sun1_KO) and two control CT26 cell lines (Sun1_Control) using CRISPR-Cas9. By performing RNA-seq on cultured cells, tumors grown in syngeneic model, and purified tumor cells from tumors grown in syngeneic model, we set out to understand how mouse Sun1 can affect immune-related pathways and immune cell infiltration and anti-PD1 efficacy in BALB/c mice.

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Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.

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Plasmodium berghei SUN1 and allantoicase interaction proteomics

Project description:SUN1 was identified in a screen for fertility genes in Plasmodium berghei. To understand its role, SUN1 was tagged with an HA tag at the endogenous locus, and SUN1 interacting proteins were characterised by affinity purification followed by mass spectrometry. This led to the identification of allantoicase as a SUN1-associated protein. Subsequent affinity interaction proteomics of HA-tagged allantoicase confirmed the interaction between these two proteins.

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Requirement for Sun1 in the expression of meiotic reproductive genes and piRNA

Project description:The inner nuclear envelope (NE) proteins interact with the nuclear lamina and participate in the architectural compartmentalization of chromosomes. The association of NE proteins with DNA contributes to the spatial rearrangement of chromosomes and their gene expression. Sun1 is an inner nuclear membrane (INM) protein that locates to telomeres and anchors chromosome movement in the prophase of meiosis. Here, we have created Sun1-/- mice and found that these mice are born and grow normally but are reproductively infertile. Detailed molecular analyses showed that Sun1-/- P14 testes are repressed for the expression of reproductive genes and have no detectable piRNA. These findings raise a heretofore unrecognized role of Sun1 in the selective gene expression of coding and non-coding RNAs needed for gemetogenesis. Total RNA was isolated from E14.5 mouse embryonic fibroblasts (MEFs) and and day 9 and 14 mouse whole testes. cDNA samples from paired (same parents) wt (Cy3-labled) and Sun1-/- (Cy5-labled) mice were mixed and hybridized.

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