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Next Generation Sequencing Facilitates Quantitative Analysis of Tumor Infiltrating CD8+T Cells Transcriptomes From Control and Manganese(II) Treated C57BL/6 Wild Type Mice

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Tumor Infiltrating CD8+T Cells Transcriptomes From Control and Manganese(II) Treated C57BL/6 Wild Type Mice

PROVIDER: PRJNA522908 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8586090.fastq.gz	Fastqsanger.gz
	SRR8586091.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Tumor Infiltrating CD8+T Cells Transcriptomes From Control and Manganese(II) Treated C57BL/6 Wild Type Mice

Project description:Purpose: The goals of this study are to compare the differentially expressed genes of tumor infiltrating CD8+T cells between control and Manganese(II) treated mice. We mainliy fouced on the differentiation of trascription and effector related genes. Methods:C57BL/6 mice were injected subcutaneously in the right flank with B16-F10 and divided into two groups followed by treatment with control (saline) or Manganese(II) respectively. After 14days, mice were euthanized with CO2 and tumor infiltrating CD8+T cells were isolated by FACS. Then RNA of sorted CD8+T cells were generated by deep sequencing using BGISEQ-500. Clean tags were mapped to the mouse genome database (GCF_000001635.25_GRCm38.p5) by HISAT (hierarchical indexing for splicing alignment for transcripts) software. Results: Using an optimized data analysis workflow, we mapped about 60 million sequence reads per sample to the mouse genome (GCF_000001635.25_GRCm38.p5). The significance of the differential expression of genes was defined by the bioinformatics service of Beijing Genomics Institute according to the combination of the absolute value of log2-Ratio ≥ 1 and false discovery rate ≤ 0.001. Conclusions: Manganese(II) enhances the function of tumor infiltrating CD8+T cells.

2021-01-19 | GSE126670 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Manganese (II) or LPS treated Wild Type BMDC Transcriptomes

Project description:Purpose: The goals of this study are to compare the different functions of manganese (II) and LPS on the activation and maturation of antigen presenting cells-BMDCs. Methods: BMDCs were generated by culturing bone marrow cells with 20 ng/ml of IL-4 (Genscript) and 20 ng/ml of GM-CSF (Genscript) at 37°C and 5% CO2 for 7 days.Then BMDCs were treated with MnCl2 (200 μM) or LPS (100 ng/ml) for 20 h. Then mRNAs were purified, sequenced and analyzed. Results: Using an optimized data analysis workflow, we compared 20339 transcripts in BMDCs. Manganese (II) induced 1677 transcripts expression with a fold change ≥1.5 and LPS induced 1555 transcripts expression with a fold change ≥1.5. Conclusion: Manganese (II) activates the production of type I IFNs and the maturation of BMDCs. But there are also some differences between functions of manganese (II) and LPS on BMDCs.

2021-05-12 | GSE126586 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Manganese (II) or LPS treated Wild Type BMDC Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Manganese (II) or LPS treated Wild Type BMDC Transcriptomes

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B. japonicum USDA110 low manganese vs. high manganese

Project description:Transcriptional profiling of B. japonicum manganese responsive cells and mur mutant responsive cells 3 independent biological materials were prepared for Wt manganese deplete, replete cultured cells and mur mutant manganese replete cultured cells

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Next Generation Sequencing Facilitates Quantitative Analysis of C57BL/6J mice.

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Expanding the Pathways of Manganese Homeostasis: Role of a Small Manganese Chaperone Protein, MntS

Project description:Escherichia coli possesses >65 small proteins of <50 amino acids, many of which are uncharacterized. We have identified a new small protein, MntS, involved in manganese homeostasis. Manganese is a critical micronutrient, serving as an enzyme cofactor and protecting against oxidative stress. Yet manganese is toxic in excess and little is known about its function in cells. Bacteria carefully control intracellular manganese levels using the transcription regulator MntR. Before this work, mntH, which encodes a manganese importer, was the only gene known to respond to manganese via MntR repression in E. coli K12. We demonstrated that mntS is another member of the MntR manganese regulon. We also identified yebN, which encodes a putative manganese efflux pump, as the first gene positively regulated by MntR in Enterobacteria. Since MntS is expressed when manganese levels are low, causes manganese sensitivity when overexpressed, and binds manganese, we propose that MntS may be a manganese chaperone. This study reveals new factors involved in manganese regulation and metabolism and expands our knowledge of how small proteins function. Two E. coli strains, MG1655 (wild type) and GSO458 (Delta-mntR) were grown to OD600 ~ 0.5 in M9 glucose media at 37 M-BM-:C and treated with 10 microM MnCl2. In the first experiment, this incubation with 10 microM MnCl2 was for 60 min and in the second experiment, it was for 10 min. RNA was extracted using the hot phenol method and cDNA prepared and hybridized according the manufacturer's instructions (Affymetrix).

2011-12-08 | E-GEOD-25318 | biostudies-arrayexpress

Expanding the Pathways of Manganese Homeostasis: Role of a Small Manganese Chaperone Protein, MntS

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Gene expression profiling of SHSY5Y cells exposed to manganese

Project description:The trace element manganese is essential for normal development for all the organisms. Overexposure of manganese may leads to multiple neuronal disorders such as Parkinson, manganism. To explore the molecular mechanism of manganese induced neurotoxicity, gene expression profiling was performed on human neuroblastoma SHSY-5Y cells. Cells were exposed to sub-lethal concentration of manganese (100 Î¼M) for 24 hrs. Our result demonstrates that manganese alter multiple biological pathways including chromatin assembly, neurogenesis and apoptotic pathways.Cells grown in 75mm2 flask. three replicates for each sample SHSY5Y cells grown in MEM:F12 media (1:1) were treated with manganese and total RNA was isolated from cells after 24 hour exposure Three replicate were used for the experiment

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Next Generation Sequencing Facilitates Quantitative Analysis of C57BL/6J mice Incisor Transcriptomes at single cell level.

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of C57BL/6J mice Incisor Transcriptomes at single cell level.

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