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Transcriptome sequencing analysis of naïve CD4+ T cells treated with NETs or control vehicle

ABSTRACT: Transcriptome sequencing analysis of naïve CD4+ T cells treated with NETs or control vehicle

PROVIDER: PRJNA678345 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13057791_1.fastq.gz	Fastqsanger.gz
	SRR13057791_2.fastq.gz	Fastqsanger.gz
	SRR13057792_1.fastq.gz	Fastqsanger.gz
	SRR13057792_2.fastq.gz	Fastqsanger.gz
	SRR13057793_1.fastq.gz	Fastqsanger.gz

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Transcriptome sequencing analysis of naïve CD4+ T cells treated with NETs or control vehicle

Project description:Purpose: We found neutrophil extracellular traps (NETs) can affect the differentiation of naïve CD4+ T cells. This sequencing aims to explore the gene profile change of neutrophil extracellular traps (NETs) on naïve CD4+ T cells. Methods: Total RNA was extracted from the T cells treated with NETs or vehicle for 72h and send to sequencing. Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina platform. Paired-end reads were then generated and evaluated for quality control. Clean raw data with high quality were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software. For quantification, FeatureCouts was used to count the read numbers mapped of each gene. Differential expression analysis between two groups (three biological replicates per condition) was performed using DESeq2 R package. Results: Using an optimized data analysis workflow, we mapped around 40 million sequence reads per sample with total mapping rate around 96%. Total 23,249 transcripts in the NETs and Vehicle group were identified. Approximately 7% of the transcripts (1675) showed differential expression between the with p value <0.05. Top differential expressed genes were then enriched based on KEGG and GO database. Altered expression genes in the most enrichment pathways were confirmed with qRT–PCR and western blot, demonstrating the high degree of sensitivity of the RNA-seq method. The top differential expressed genes provide new insigts for the mechanism of T cell differentiation affected by NETs. Conclusions: Our study represents the first detailed analysis of naïve CD4+ T cells treated with NETs. Most differentital expressed genes were enriched in metabolic pahtways, which prompted us to further explore the related mechanism of the novel phenotype.

2021-12-10 | GSE161464 | GEO

RNA Sequencing reveals transcriptome profiling of HUVECs in response to NETs ± defibrotide

Project description:We reported the application of RNA sequecing to broadly understand the pathways associated with HUVECs exposed to vehicle, NETs, or NETs + defibrotide. We identified 440 differentially expressed genes (300 upregulated) in HUVECs upon NET stimulation as compared with vehicle. Conversely, there were 229 differentially expressed genes (192 downregulated) when the NETs + defibrotide group was compared to NETs alone.

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Human Fetal and Adult Peripheral Naïve CD4+ T cells and CD4+CD25+ Treg cells

Project description:We compared differences in fetal and adult T cells by performing whole genome profiling on sort-purified T cells (naïve CD4+ and Treg cells) from human fetal specimens (18-22 gestational weeks) and adult specimens (age 25-40 years old). Fetal and Adult Naïve CD4+ T cells phenotype: CD3+CD4+CD45RA+CCR7+CD27+, Fetal and Adult CD4+CD25+ Treg phenotype: CD3+CD4+CD25bright Four different groups were analyzed: Fetal Naïve CD4+ T cells, Adult Naïve CD4+ T cells, Fetal Treg cells, Adult Treg cells. For each group three independent donors were analyzed.

2010-12-17 | E-GEOD-25087 | biostudies-arrayexpress

Strain-specific CNV in zebrafish treated with PCB-126, vehicle control, or untreated

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Bcl6 controlled gene expression in naïve CD4 T cells (Tf0)

Project description:Gene expression data from wild-type and Bcl6-/- naive CD4 T cells In order to find genes regulated by Bcl6 in follicular helper T cells Naïve CD4 T cells were sorted from wild-type (WT) and T cell-specific conditional Bcl6-/- (KO) mice-- 8 samples, 4 WT and 4 KO

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Bcl6 controlled gene expression in naïve CD4 T cells (Tfh)

2015-04-08 | E-GEOD-67623 | biostudies-arrayexpress

Human Fetal and Adult Peripheral Naïve CD4+ T cells and CD4+CD25+ Treg cells

2010-12-17 | GSE25087 | GEO

Comparison of gene expression in mouse CD4 naïve and activated T-cells

Project description:Gene expression changes when naïve T-cells are stimulated with antigen. We have stimulated these cells with surrogate antigens (aCD3-aCD28 coated beads) for 48 hours, and then did microarray experiment to identify differentially exprssed genes in the two conditions CD4 naïve T-cells from C57/Bl6 mouse were stimulated (activated) with aCD3-aCD28 coated beads for 48 hours and used for microarray experiment

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Rheumatoid arthritis patients, both newly diagnosed and methotrexate treated, show more DNA methylation differences in CD4+ memory than in CD4+ naïve T cells

Project description:Differences in DNA methylation have been reported in B and T lymphocyte populations, including CD4+ T cells, isolated from rheumatoid arthritis (RA) patients when compared to healthy controls. CD4+ T cells are a heterogeneous cell type with subpopulations displaying distinct DNA methylation patterns. In this study, we investigated DNA methylation using reduced representation bisulfite sequencing in two CD4+ T cell populations (CD4+ memory and naïve cells) in three groups: newly diagnosed, disease modifying antirheumatic drugs (DMARD) naïve RA patients (N=11), methotrexate (MTX) treated RA patients (N=18), and healthy controls (N=9) matched for age, gender and smoking status. Analyses of these data revealed significantly more differentially methylated positions (DMPs) in CD4+ memory than in CD4+ naïve T cells (904 vs 19 DMPs) in RA patients compared to controls. The majority of DMPs (72%) identified in newly diagnosed and DMARD naïve RA patients with active disease showed increased DNA methylation (39 DMPs), whereas most DMPs (80%) identified in the MTX treated RA patients in remission displayed decreased DNA methylation (694 DMPs). Interestingly, we also found that about one third of the 101 known RA risk loci overlapped (+/- 500 kb) with the DMPs. Notably, introns of the UBASH3A gene harbour both the lead RA risk SNP and two DMPs in CD4+ memory T cells. Our results suggest that RA associated DNA methylation differences vary between the two T cell subsets, but are also influenced by RA characteristics such as disease activity, disease duration and/or MTX treatment.

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H3K27me3 ChIP-seq of naïve CD4 T cells

Project description:H3K27me3 ChIP-seq of naïve CD4 T cells

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