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RNA-seq data from double positive thymocyte and CD4 or CD8 single positive spleen T cell

ABSTRACT: RNA-seq data from double positive thymocyte and CD4 or CD8 single positive spleen T cell

PROVIDER: PRJNA448448 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6927752.fastq.gz	Fastqsanger.gz
	SRR6927753.fastq.gz	Fastqsanger.gz
	SRR6927754.fastq.gz	Fastqsanger.gz
	SRR6927755.fastq.gz	Fastqsanger.gz
	SRR6927756.fastq.gz	Fastqsanger.gz

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RNA-seq data from double positive thymocyte and CD4 or CD8 single positive spleen T cell

Project description:Control RNA-seq data for thymocyte and spleen T cell.

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Paxbp1 is indispensable for the survival of CD4 and CD8 double-positive thymocytes

Project description:The lifespan of double-positive (DP) thymocytes is critical for intrathymic development and shaping the peripheral T cell repertoire. However, the molecular mechanisms that control DP thymocyte survival remain poorly understood. Paxbp1 is a conserved nuclear protein that has been reported to play important roles in cell growth and development. Its high expression in T cells suggests a possible role in T cell development. Here, we observed that deletion of Paxbp1 resulted in thymic atrophy in mice lacking Paxbp1 in the early stages of T cell development. Conditional loss of Paxbp1 resulted in fewer CD4+CD8+ DP T cells, CD4 and CD8 single positive (SP) T cells in the thymus, and fewer T cells in the periphery. Meanwhile, Paxbp1 deficiency had limited effects on the CD4-CD8- double negative (DN) or immature single-positive (ISP) cell populations. Instead, we observed a significant increase in the susceptibility of Paxbp1-deficient DP thymocytes to apoptosis. Consistent with this, RNA-Seq analysis revealed a significant enrichment of the apoptotic pathway within differentially expressed genes in Paxbp1-deficient DP cells compared to control DP cells. Together, our results suggest a new function for Paxbp1, which is an important mediator of DP thymocyte survival and critical for proper thymic development.

2023-06-14 | GSE233211 | GEO

RNA-seq of Smarca5-deficient CD4/CD8 double-positive thymocytes isolated from 6-week mouse thymi and their comparison with wild-type and TP53-null controls.

Project description:Here we utilized a conditional knock-out mouse model to investigate the role of Smarca5, an ISWI subfamily chromatin remodeling ATPase, during thymocyte development using hCD2-iCre transgene. We did transcriptional profiling of FACS-sorted CD4/CD8 double-positive thymocytes as this thymic population was persistent yet strongly underrepresented in adult 6-week mutant thymi. Controls included age-matched CD4/CD8 double-positive thymocytes from wild-type and tumor suppressor protein Trp53-null mice. For comparison, the Smarca5/Trp53-double-deficient thymocytes included in the experiment were partially rescued upon loss of Trp53.

2019-04-01 | E-MTAB-7758 | biostudies-arrayexpress

Microarray analysis of gene expression in CD4+CD8+ double pos (DP) thymocytes upon depletion of Ubiquitin specific protease 8

2014-03-04 | GSE55517 | GEO

Transcription profiling of mouse SOX13 mutants to identify Sox13 regulated genes in CD4+CD8+ double positive thymocytes

Project description:ab and gd T cells originate from a common, multi-potential precursor population in the thymus, but the molecular mechanisms regulating this lineage fate decision process are unknown. We have identified Sox13 as a gd-specific gene in the immune system. Using Sox13 transgenic mice, we show that SOX13 promotes gd T cell development while opposing ab T cell differentiation. Conversely, mice deficient in Sox13 expression exhibited impaired development of gd T cells, but not ab T cells. One mechanism of SOX13 function is the inhibition of WNT/TCF signaling, suggesting that differential WNT/TCF activity is an essential parameter for this binary cell fate choice. Experiment Overall Design: CD4+CD8+ double positive thymocyte subsets were sorted by FACS using total pooled thymocytes from minimum of two mice and immediately lysed in Trizol. Comparison groups in each experiment were DP thymocytes from Sox13 transgenic mice and wild type B6 littermate controls. Gene expression profiling was performed according to the manufacturerâ??s protocol (Affymetrix). Labeled cRNA (from total RNA) was generated and applied to Affymetrix Mu11K(A and B) (expt 1) or muU74Av2 (expt 2) microarrays. Results were analyzed using Microarray Analysis Software v4 and v5 (Affymetrix).

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Microarray analysis of gene expression in CD4+CD8+ double pos (DP) thymocytes upon depletion of Ubiquitin specific protease 8

Project description:T-cell-specific deletion of USP8 (USP8ffCD4Cre) revealed that USP8 is required for thymocyte transition to the CD4+ and CD8+ single positive (SP) stages. To evaluate underlying mechanisms, gene expression profilling was performed in CD4+CD8+ double pos thymocytes derived from control (USP8ff and USP8ffCD4Cre) mice. Microarray analysis of two groups of USP8fl/fl and USP8fl/flCD4Cre thymocytes. Material from two mice was combined for each group (eight mice in total).

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2020-12-17 | GSE156070 | GEO

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Project description:Mouse thymocytes can be classified into four major subsets based on expression of CD4 and CD8 co-receptors. CD4-CD8- (double negative, DN) cells become CD4+CD8+ (double positive, DP) cells following productive T cell receptor (TCR) beta chain rearrangement. A small proportion of DP cells are selected through interaction of clonal TCRalpha/beta and MHC self peptide complex expressed on thymic stromal cells. DP cell expressing MHC class I-restricted TCR become CD4-CD8+ cells, which will finally differentiate into cytotoxic T cells, while MHC class II restricted selection generates CD4+CD8- helper lineage T cells. We used microarrays to identify genes important for thymocyte differentiation and lineage determination by profiling gene expression in different thymocyte subsets.

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Spleen vs Liver - cDNA - Double

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Chromatin organizer SATB1 controls the cell identity of CD4+ CD8+ double-positive thymocytes by compacting super-enhancers

Project description:CD4+ and CD8+ double-positive (DP) thymocytes are at a critical stage during the T cell development in thymus. DP cells rearrange the T cell receptor gene Tcra to generate T cell receptors with TCR. Then DP cells differentiate into CD4 or CD8 single-positive (SP) thymocytes, Regulatory T cells, or invariant nature kill T cells (iNKT) according to the TCR signal. Chromatin organizer SATB1 is highly expressed in DP cells and plays an essential role in regulating Tcra rearrangement and differentiation of DP cells. Here we explored the mechanism of SATB1 orchestrating gene expression in DP cells. Single-cell RNA sequencing assay of SATB1-deficient thymocytes showed that the cell identity of DP thymocytes was changed, and the genes specifically highly expressed in DP cells were down-regulated. ChIP-seq and ATAC-seq data showed the similar tendency. The super-enhancers regulate the expressions of the DP-specific genes, and the SATB1 deficiency reduced the super-enhancer activity. Hi-C data showed that interactions in super-enhancers and between super-enhancers and promoters decreased in SATB1 deficient thymocytes. We further explored the regulation mechanism of two SATB1-regulating genes, ETS2 and Bcl6, in DP cells and found that the knockout of the super-enhancers of these two genes impaired the development of DP cells. Our research reveals that SATB1 globally regulates super-enhancers of DP cells and promotes the establishment of DP cell identity, which helps understand the role of SATB1 in thymocyte development.

2021-09-02 | GSE182995 | GEO

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