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

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

PROVIDER: PRJNA889806 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21878301.fastq.gz	Fastqsanger.gz
	SRR21878302.fastq.gz	Fastqsanger.gz
	SRR21878303.fastq.gz	Fastqsanger.gz
	SRR21878304.fastq.gz	Fastqsanger.gz
	SRR21878305.fastq.gz	Fastqsanger.gz

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

Project description:The goal of this study was to compare the gene expression program of iNKT1 cells in the thymus, liver and spleen. To identify iNKT1 cells we created Tbx21Cre bacterial artifical chromosome transgenic mice with a Rosa26-floxed-stop-YFP reporter. We examined gene expression by RNA-sequencing in sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from the thymus, liver and spleen. 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 from all tissues had very similar gene expression programs but that there were subtle difference in each tissue that may have relevance for survival and function in these tissues.

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