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Analysis of transcriptional differences between TER cells, B lymphocytes and embryonic liver nucleated erythrocytes

ABSTRACT: Analysis of transcriptional differences between TER cells, B lymphocytes and embryonic liver nucleated erythrocytes

PROVIDER: PRJNA833663 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19019087_1.fastq.gz	Fastqsanger.gz
	SRR19019087_2.fastq.gz	Fastqsanger.gz
	SRR19019088_1.fastq.gz	Fastqsanger.gz
	SRR19019088_2.fastq.gz	Fastqsanger.gz
	SRR19019089_1.fastq.gz	Fastqsanger.gz

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Analysis of transcriptional differences between TER cells, B lymphocytes and embryonic liver nucleated erythrocytes

Project description:To verify the origin of TER cells from B lymphocytes，we profiled the differentially expressed genes in CD19+/TER119+/CD45+ cells by RNA-sequencing, with fetal liver-derived CD71+/TER119+/FSChigh cells (CECs) as erythroblast control and CD19+/TER119- cells as B-cell control.

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Project description:Bone marrow and peripheral blood were obtained from patients after myocardial infarction. Erythrocytes were removed by NH4CL lysis to finally obtain nucleated bone marrow cells and peripheral blood leukocytes. After RNA isolation, RNA from three patients was pooled and the RNA expression profile of both organism parts were compared.

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Project description:Chicken erythrocytes are nucleated cells often referred to as transcriptionally inactive, although the epigenetic changes and chromatin remodeling that mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here we characterized the changes in gene expression, chromatin accessibility, genome organization, and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and found a complex chromatin reorganization at different genomic scales. We identified a robust decrease in transcription in erythrocytes. Nevertheless, a set of genes maintains their expression in erythrocytes, including genes involved in RNA pol II promoter-proximal pausing. Erythrocytes exhibit an inverted nuclear architecture and reposition euchromatin towards the nuclear periphery together with the paused RNA polymerase. In erythrocytes, chromatin domains are partially lost genome-wide except at mini domains retained around paused promoters. Our results suggest that promoter-proximal pausing of the RNA pol II participates in the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.

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Next Generation Sequencing Facilitates Quantitative Analysis of Ter cells Transcriptomes

Project description:Purpose:The purpose of this study is to detect genes Ter-119+CD45−Lin− cells sorted from spleen of tumor-bearing mice and the control cells. Gene expression differences between seven samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: The seven cell subsets were isolated from spleen of tumor-bearing mice, embryonic liver (E14.5) and bone marrow of wild type mice by cell sorter respectively. Cells with purity >98% were used for subsequent experiments. The cell subsets RNA profiles were generated by deep sequencing,using Illumina. Results: Genes with FPKM values above 10.0 in the cell groups were used for subsequent analysis. Single linkage clustering analysis between the groups and prcomp function-based PCA analysis on the expression matrix were performed by R software. We found that the tumor-induced Ter-119+CD45−Lin− cells expressed the transcriptional factors and functional genes associated with erythrocyte and megakaryocyte development, but not myeloid cells differentiation.

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Project description:Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in erythrocytes. Methods: Red blood cells were obtained from cardiac puncture, mixed with 100µl Aster Jandl citrate-based anticoagulant and subsequently diluted in 2 ml of phosphate buffer saline (PBS) with 2mM EDTA. This suspension was layered with 1.5 ml Ficoll-paque PLUS (GE Healthcare) and centrifuged at 400g for 30 minutes at room temperature with minimal acceleration and brake. The red blood cell containing pellet was washed twice with PBS 2mM EDTA and lysed for RNA extraction. The purity of each sample was checked by flow cytometry to assess the relative contamination of Ter199+ red blood cells with CD41+ platelets, CD45+ lymphocytes and DRAQ5+ (Thermo Fisher Scientific) nucleated cells. Red blood cell suspensions used for RNAseq were > 99.8% pure. RNA was extracted with Qiagen RNA extraction kit.

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