Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE278708 | GEO | 2024/10/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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.

2024-10-16 | GSE279288 | GEO

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.

2024-10-10 | GSE278707 | 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).

2022-10-13 | GSE215128 | GEO

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.

2022-10-15 | GSE215338 | GEO

RNAseq analysis of thymic CD4-CD8- double-negative (DN) invariant NKT cells from CD4+CD8+ double-positive (DP)-specific Rag2-conditional knock-out mice

Project description:We report the identification of DN NKT cells developed from DN stage thymocytes. We analyzed the gene expression profiles of NKT cells that have developed from DN stage thymocytes isolated from DP-specific E8III-Cre transgenic Rag2-floxed mouse strain, and NKT cells developed from DP thymocytes sorted as YFP-reporter positive NKT cells that were isolated from E8III-Cre transgenic Rosa26-loxP-STOP-loxP mouse.

2016-11-30 | GSE89532 | GEO

Gene expression profiling in Tie-2-Etv2 endothelial and/or hematopoietic precursors

Project description:Etv2 transgene was expressed from ROSA26 locus by removing floxed STOP cassette by Tie-2 Cre transgene. VE-Cad+/CD45= or VE-Cad+/CD45+ cells were sorted from control or tie-2-Etv2 E11.5 embryos (YS;yolk sac and Emb;embryo proper)and compared for gene expression in duplicate.

2012-05-10 | GSE36516 | GEO

RNAseq comparing mouse Cre-loxP-induced EWSR1-ATF1 expression from Rosa26 versus Ewsr1-Atf1 translocation

Project description:Mice formed tumors either after a TATCre-induced floxed-STOP removal from an EWSR1-ATF1 human cDNA expression vector targeted to the Rosa26 endogenous pseudogene or after an Hprt-Cre-initiated translocation between Ewsr1 and Atf1 genes on chromosomes 11 and 15. From total RNA, libraries were generated using the RiboZero method and sequenced on an Ilumina NovaSeq instrument to permit comparison to each other.

2020-09-30 | GSE158725 | GEO

mRNA-seq of Myc and Yap1-activated mouse lung tumors and controls

Project description:mRNA-seq for expression profiling of Myc and Yap1 activated mouse lung tumors and controls. 4 cohorts of lung tumors induced through nasal instillation of Cre/sgRNA(MS2)-encoding lentivirus in mice carrying conditional P53 loss (P53 F/F), oncogenic Kras (Kras LSL-G12D/+), and CRISPRa/SAM construct (Rosa26(LSL-SAM) or YFP reporter (Rosa26(LSL-YFP): 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(Myc) (PPKS/M); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(Yap1) (PPKS/Y); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(non-targeted) (PPKS/NT); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-YFP) / lenti(CMV-Cre/U6-sgRNA(non-targeted) (PPKY/NT)

2022-08-30 | E-MTAB-11122 | biostudies-arrayexpress