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Analysis of gene expression changes in fetal erythroid cells obtained from mice with Csnk2b gene conditional deletion in the hematopoietic system.

ABSTRACT: Analysis of gene expression changes in fetal erythroid cells obtained from mice with Csnk2b gene conditional deletion in the hematopoietic system.

PROVIDER: PRJNA666157 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12730415.fastq.gz	Fastqsanger.gz
	SRR12730416.fastq.gz	Fastqsanger.gz
	SRR12730417.fastq.gz	Fastqsanger.gz
	SRR12730418.fastq.gz	Fastqsanger.gz
	SRR12730419.fastq.gz	Fastqsanger.gz

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Analysis of gene expression changes in fetal erythroid cells obtained from mice with Csnk2b gene conditional deletion in the hematopoietic system.

Project description:Protein Kinase CK2 is a pleiotropic and constitutively expressed enzyme (phosphotransferase) usually present as a tetrameric complex of two catalytic alpha and two regulatory beta subunits. Alpha and beta proteins can also work independently from the holoenzyme exerting different functions on other protein targets. It is well known the CK2 role in promoting cell survival and proliferation and in sustaining the growth of many hematological malignances. However, its physiological role in hematopoiesis, in particular in erythropoiesis is still unknown. Our analysis was focused on the hematopoietic functions of the beta subunit through the generation of conditional KO mice for Csnk2b gene in the hematopoietic system. Our purpose was to asses if CK2b plays a role in the development of erythroid cells. To this aim, we performed a mRNA sequencing analysis of erythroid TER119+ cells purified from control (Csnk2b+/+) and KO (Csnk2b-/-) embryos and here we report a complete list of the genes resulted to be differentially expressed.

2022-09-30 | GSE158665 | GEO

Analysis of gene expression changes in B cells upon Csnk2b conditional deletion

Project description:Protein kinase CK2, a tetrameric enzyme composed by 2 catalitic alpha and 2 regulatory beta subunits, supports malignant B cell lymphocyte growth, however, its physiological role in B lymphopoiesis is still unknown. With this analysis we intended to assess if CK2 plays a role in peripheral B cell development and to do this we compared the mRNA from Csnk2b+/+ (WT) and Csnk2b-/- (KO) purified splenic B cells. Here we report a list of all genes identified as differentially expressed between WT and KO B cells.

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Project description:The developing erythroid cells require highly coordinated gene expression and metabolism. By comparing the proteomic and transcriptomic changes in human hematopoietic stem/progenitor cells (HSPCs) and lineage-committed erythroid progenitors (ProEs), and uncover pathways related to mitochondrial biogenesis enhanced through post-transcriptional regulation. Two principal mitochondrial factors TFAM and PHB2 are tightly regulated at the protein level and indispensable for mitochondria and erythropoiesis. To determine the role of TFAM in mitochondrial function during erythroid development, we generated Tfam conditional knockout (KO) mice by an erythroid-specific EpoR-Cre allele. We isolated the CD71+Ter119+ embryonic day (E)13.5 fetal liver erythroid cells by FACS sorting, and performed RNA-seq transcriptional profiling analysis.

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Project description:Exosc8 and Exosc9 are components of the exosome that establish a barricade to erythroid maturation. Here, we knocked down Exosc8 in fetal liver-derived erythroid progenitor cells to determine the cohort of Exosc8-regulated genes in erythroid cells. Freshly isolated fetal liver progenitor cells were infected with retrovirus expressing shRNA targeting either luciferase or Exosc8. Total RNA was isolated from these cells after 3 days ex-vivo culture, during which the cells underwent erythroid maturation.

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Project description:The S1 and S3 erythroid developmental subsets were isolated using flow cytometry and the cell surface markers CD71 and Ter119 as described by Pop et. al. 2010 (PMID: 20877475) Expression profiles for S1 and S3 subsets were generated using Affymetrix GeneChips. Results were used to identify genes that are differentially expressed during erythropoiesis. Single cell suspensions were prepared by mechanically dissociating whole fetal livers obtained from E12.5 to E13.5 Balb/C mouse embryos. Cells were stained for CD71, Ter119, and a cocktail containing lineage-specific antibodies. S1 and S3 erythroid developmental subsets were identified and isolated using flow cytometric sorting as described by Pop et. al. 2010 (PMID: 20877475). S1 and S3 subsets were isolated on 3 seperate days to generate total RNA (biological replicates). 20 ng of total RNA from each biological replicate was converted to cDNA, linearly amplified and biotinylated using Ovation reagents (Nugen, San Carlos, CA). Samples were hybridized to Mouse Genome 430 2.0 Arrays (Affymetrix, Santa Clara, CA). Microarray suite 5 (MAS5) processed sample data were normalized to the average of 18SRNA (AFFX-18SRNAMur/X00686_M_at), GAPDH (AFFX-GapdhMur/M32599_3_at) and M-NM-2-actin (1419734_at) expression values. These gene expression profiles were performed as part of the manuscript by Shearstone et. al. Global DNA Demethylation During Erythropoiesis In Vivo

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