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Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation

ABSTRACT: Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation

PROVIDER: PRJNA946742 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23920416_1.fastq.gz	Fastqsanger.gz
	SRR23920416_2.fastq.gz	Fastqsanger.gz
	SRR23920417_1.fastq.gz	Fastqsanger.gz
	SRR23920417_2.fastq.gz	Fastqsanger.gz
	SRR23920418_1.fastq.gz	Fastqsanger.gz

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Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation

Project description:To unbiasedly characterize the spatial transcriptomics landscape of murine small intestine damage and repair, we performed a time-series spatial transcriptional analysis of total small intestinal tissue during the course of irradiation damage from mice receiving standard diet. Additionally, to understand the role of LXR activation during damage and repair, we also collected small intestine tissues from mice fed with GW3965 diet.

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Gene expression profiling of small intestine (SI) NKp46+RORgt+ and NKp46+RORgt- Innate Lymphoid Cells (ILCs)

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Gene expression profiling of small intestine (SI) NKp46+RORgt+ and NKp46+RORgt- Innate Lymphoid Cells (ILCs)

Project description:The aim of this study was to analyze the global transcriptional profiles of small intestine (SI) Innate Lymphoid Cells (ILCs) expressing the NK cell marker NKp46. Based on differential expression of the RORgt transcription factor SI NKp46+ ILCs can be divided in NKp46+RORgt- and NKp46+RORgt+ cells. While NKp46+RORgt- cells produce IFN-g, like conventional Natural Killer (NK) cells, NKp46+RORgt+ cells secrete IL-22, like Lymphoid Tissue inducer (LTi) cells. We compared the global transcriptional profiles of both NKp46+RORgt- and NKp46+RORgt+ cells to conventional splenic NK cells and to SI NKp46-RORgt+ cells, which contain adult LTi cells. By following this approach, we showed that SI NKp46+RORγt- ILCs correspond to SI NK cells. We also identified a transcriptional program conserved in adult SI NKp46+RORγt+, NKp46-RORγt+ ILCs and fetal LTi. The various ILC cell populations analyzed in this study were isolated from C57BL/6 RORc(gt)+/GFP reporter mice. SI NKp46+RORγt- (NKp46+GFP-) cells, SI NKp46+RORγt+ cells (NKp46+GFPlow and NKp46+GFPhigh cells) and NKp46-RORγt+ ILCs, including adult LTi cells , were sorted by flow cytometry from CD3- lamina propria cells of small intestine (SI) of RORc(γt)+/GFP reporter mice . Splenic NKp46+RORγt- (NKp46+GFP-) cells were also sorted as the reference for conventional NK cells. Two replicates of each populations were produced and analyzed.

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