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Transcriptomic profiling of ex vivo isolated CD3+CD4+ T cells from spleens of colitic Rag-/- mice received naïve ERαfl/fl and CD4CreERαfl/fl CD4+ T cells

ABSTRACT: Transcriptomic profiling of ex vivo isolated CD3+CD4+ T cells from spleens of colitic Rag-/- mice received naïve ERαfl/fl and CD4CreERαfl/fl CD4+ T cells

PROVIDER: PRJNA419546 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6317711.fastq.gz	Fastqsanger.gz
	SRR6317712.fastq.gz	Fastqsanger.gz
	SRR6317713.fastq.gz	Fastqsanger.gz
	SRR6317714.fastq.gz	Fastqsanger.gz

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Transcriptomic profiling of ex vivo isolated CD3+CD4+ T cells from spleens of colitic Rag-/- mice received naïve ERαfl/fl and CD4CreERαfl/fl CD4+ T cells

Project description:To study the role of estrogen receptor alpha (ERα) in T cell mediated inflammation, colitis was induced in Rag-/- mice by injecting FACS sorted CD4 T cells from control (ERαfl/fl) and ERα deficient (CD4CreERαfl/fl). After 8 weeks of injection, the CD4+ T cells were FACS sorted from Rag-/- spleens. RNA extraction was carried out and libraries were prepared using Illumina TruSeq RNA sample Preparation kit according to the manufacturer’s instructions.

2018-03-23 | GSE107284 | GEO

RNA seq of vhlfl/fl cd4 cre, hif1afl/fl vhlfl/fl cd4 cre and WT CD4 T cells before and after anti-CD3/CD28 stimulation

Project description:Purpose: We compared the transcriptomes of murine CD4 T cells lacking either the vhl gene ( vhlfl/fl cd4 cre (vhl cKO) ) or both vhl and hif1a (hif1afl/fl vhlfl/fl cd4 cre (dcKO)) with WT controls before and 24 h after T cell receptor stimulation using anti-CD3/CD28. Results: Using an optimized data analysis workflow, about 45-60 million sequence reads per sample to the mouse genome (build mm10) and identified ca 12500 transcripts in the CD4 T cells of WT and mutant mice after performing HISAT2 alignements to the mm10 reference. Conclusion: the segregation of the transcriptome of unstimulated WT CD4 T cells as compared to the other groups. Within the TCR-stimulated groups the gene expression of vhl cKO CD4 T cells differed to that of WT and vhl hif1a dcKO CD4 T cells which showed in comparison important similarity between them

2022-06-01 | GSE190791 | GEO

Gut microbiota analysis of colitic SD rats

Project description:Fecal samples collected on day 5 from randomly selected colitic SD rats were analyzed for gut microbiota by sequencing the V4 region of the 16S rRNA gene. The orally administered Dex-P-laden NPA2 coacervate (Dex-P/NPA2) significantly restores the diversity of gut microbiota compared with colitic SD rats in the Dex-P/PBS group and the untreated colitic rats (Control).

2021-11-06 | GSE167138 | GEO

RNA seq of vhlfl/fl cd4 cre, hif1afl/fl vhlfl/fl cd4 cre and WT CD4 T cells before and after anti-CD3/CD28 stimulation

Project description:RNA seq of vhlfl/fl cd4 cre, hif1afl/fl vhlfl/fl cd4 cre and WT CD4 T cells before and after anti-CD3/CD28 stimulation

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Single cell RNA-seq of CDH5+ Rela fl/fl murine hepatic CD4+ T-cells

Project description:Single cell RNA-seq of CDH5+ Rela fl/fl murine hepatic CD4+ T-cells

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Production of cytokines by CD4+CAR+ T-cells in spleens

Project description:The aim of the study was to compare and contrast cytokine production by CD4+ chimeric antigen receptor + T-cells and putative myeloid derived suppressor cell populations (CD11b+Gr-1 hi and lo) in the spleens of Balb/c mice which had received a transfer of CD19 specific second-generation CAR T-cells 56 days previously following cyclophosphamide pre-conditioning. Splenocytes from four individual mice were pooled, incubated with antibodies to CD4, CD34 (CAR), CD11b, Gr-1 and sorted using flow cytometric cell sorting for CD4+CD34+, Gr-1 and the negative cell fraction. Total RNA was isolated and samples loaded in duplicate in the array. Data was normalized to global expression levels.

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RNA-seq of CD4 T cells from the lungs of M. tuberculosis infected WT and vhl fl/fl cd4 cre mice

Project description:RNA-seq of CD4 T cells from the lungs of M. tuberculosis infected WT and vhl fl/fl cd4 cre mice

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RNA-seq of CD4 T cells from the lungs of M. tuberculosis infected WT and vhl fl/fl cd4 cre mice

Project description:Purpose: We compared the transcriptomes of mouse CD4 T cells lacking the vhl gene ( vhlfl/fl cd4 cre= vhl cKO) with WT controls from the lungs of mice 8 weeks after aerosol infection with Mycobacterium tuberculosis. Results: Using an optimized data analysis workflow, between 40-55 million sequence reads per sample to the mouse genome (build mm10) and identified 14700 transcripts in the CD4 T cells of WT and mutant mice after performing HISAT2 alignements to the mm10 reference. Conclusion: The transcriptome of WT anf vhl cKO was compared. Groups did cluster differentially with regards to their transcript abundance. The WT group has enriched DNA synthesis/ proliferation pathways whereas the Vhl cKO was enriched in hypoxia pathways. Transcripts assocaited with T cell differentiation were increased in WT group while T cell inhibitory molecules was elevated in the transcriptome of vhl cKO CD4 T cells.

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