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Exploring the organ specific expression pattern of CD4+iNKT1 cells of C57BL/6 and BALB/c mice.

ABSTRACT: Exploring the organ specific expression pattern of CD4+iNKT1 cells of C57BL/6 and BALB/c mice.

PROVIDER: PRJNA672096 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12900351.fastq.gz	Fastqsanger.gz
	SRR12900352.fastq.gz	Fastqsanger.gz
	SRR12900353.fastq.gz	Fastqsanger.gz
	SRR12900354.fastq.gz	Fastqsanger.gz
	SRR12900355.fastq.gz	Fastqsanger.gz

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Exploring the organ specific expression pattern of CD4+iNKT1 cells of C57BL/6 and BALB/c mice.

Project description:iNKT cells are generated in thymus and settle all organs and tissues in mice. We used RNA high throughput sequencing to identify genes that displayed an organ specific expression by comparing iNKT1 cells of thymus, liver, blood, and spleen origin, respectively. We observed organ specific expression of a variety of genes that might reflect specialized functional adaptations connected to the unique micro-environments of the investigated organs.

2021-11-18 | GSE160144 | GEO

RNA-seq of Tgfbr2-deficient thymic iNKT1 cells

Project description:The goal of this study was to identify genes that are regulated by TGF-b-signaling in thymic iNKT1 cells. To specifically target Tgfbr2 deletion to iNKT1 cells we created Tbx21Cre bacterial artifical chromosome transgenic mice with a Rosa26-floxed-stop-YFP reporter and floxed alleles of Tgfbr2 . We examined gene expression by RNA-sequencing in sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from Ctrl (Tbx21Cre; Rosa26-YFP+) and cKO (Tbx21Cre; Rosa26-YFP+; Tgfbr2F/F) mice. Reads were aligned to the mm10 reference genome using STAR v2.5.2. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 3 independent replicates by EdgeR. We found that TGF-b was required for normal numbers of iNKT1 cells and induced a classic TGF-b gene program in thymic iNKT1 cells but did not regulate expression of Tbx21 (T-bet).

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Tbet dysregulation compensates for Ets-deficiency in iNKT1 cells

Project description:The goal of this study was to compare the gene expression program of liver iNKT1 cells from Control mice to those with a postselection deletion of the transcription factor Ets1 and heterozybous deletion of Tbx21. Ets1-floxed and Tbx21-floxed alleles were deleted in iNKT1 cells using Tbx21Cre bacterial artifical chromosome transgenic mice that also carry a Rosa26-floxed-stop-YFP reporter. Control iNKT1 cells were Tbx21Cre+ Rosa26-floxed-stop-YFP reporter+ and cKOHet iNKT cells were Tbx21Cre+ Ets1F/F Tbx21F/+ Rosa26-floxed-stop-YFP reporter+. The differentially expressed genes were compared to those in liver iNKT1 cells with postselection deletion of Ets1 only. We examined gene expression by RNA-sequencing of sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from the liver. Reads were aligned to the mm10 reference genome using Tophat v 2.1.0. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 3 independent replicates by EdgeR. We found that iNKT1 cells lacking Ets1 upregulated Tbx21 and its protein Tbet, many Tbet target genes, and CD8 effector T cell associated genes.

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RNA-seq of wild-type iNKT1 cells from thymus, liver and spleen

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Ets1 dampens expression of Tbet and CD8- or NK-like effector programing in postselection iNKT1 cells [RNA-seq]

Project description:The goal of this study was to compare the gene expression program of thymic and liver iNKT1 cells from Control mice to those with a postselection deletion of the transcription factor Ets1. Ets1-floxed alleles were deleted in iNKT1 cells using Tbx21Cre bacterial artifical chromosome transgenic mice that also carry a Rosa26-floxed-stop-YFP reporter. Control iNKT1 cells were Tbx21Cre+ Rosa26-floxed-stop-YFP reporter+. We examined gene expression by RNA-sequencing of sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from the thymus and liver. Reads were aligned to the mm10 reference genome using Tophat v 2.1.0. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 3 independent replicates by EdgeR. We found that iNKT1 cells lacking Ets1 upregulated Tbx21 and its protein Tbet, many Tbet target genes, and CD8 effector T cell associated genes.

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Ets1 dampens expression of Tbet and CD8- or NK-like effector programing in postselection iNKT1 cells [scRNA-seq]

Project description:The goal of this study was to compare the gene expression program of thymic iNKT1 cells from Control mice to those with a postselection deletion of the transcription factor Ets1 at the single cell level. Ets1-floxed alleles were deleted in iNKT1 cells using Tbx21Cre bacterial artifical chromosome transgenic mice that also carry a Rosa26-floxed-stop-YFP reporter. Control iNKT1 cells were Tbx21Cre+ Rosa26-floxed-stop-YFP reporter+. We isolated all thymic YFP+ cells from Control and cKO mice and processed for scRNA-seq using the 10X Genomics Chromium. Data was processed using the Cell Ranger program for 10X Genomics. . We found that iNKT1 cells lacking Ets1 upregulated Tbx21 and its protein Tbet, many Tbet target genes, and CD8 effector T cell associated genes.

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