Gene expression analysis of in vitro activated B cells from C57BL/6 and Ackr4-deficient mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE138175 | GEO | 2019/12/21
REPOSITORIES: GEO
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Project description:Purpose: The goal of this study was to compare exome sequences of Ackr4-deficient mice with C57BL/6 wildtype sequences to understand phenotypic differences which can not be explained by Ackr4-deficiency. Methods: Tail DNA of one wild-type (WT, C57BL/6) and atypical chemokine receptor 4 knockout (Ackr4−/−) mice was sequenced by exome sequencing using an Illumina NovaSeq 6000 sequencing system (2x 100bp). After demultiplexing (Illumina bcl2fastq 2.19) and adapter trimming (Skewer, 0.2.2), the trimmed reads were aligned with to the murine genome (mm10) with Burrows-Wheeler Aligner (BWA-mem 0.7.2-cegat). Reads aligned to multiple sides with the same mapping score were discarded. Further, duplicated reads were removed with SAMtool 0.1.18. Genetic variants were identified with Verscan 2.4.2-cegat and variants with a frequency of ≥ 2% were annotated with SnpEff (version 4.2 with GRCm38.75). Results: 100,000 to 140,000 million sequence reads per mouse were mapped to the mouse genome (build mm10). Each mouse had approx. 20,000 variants (insertions, deletions, SNPs) compared to the reference genome. In Ackr4-/- mice, 3,367 variants were present in both mice analysed, yet not detected in the C57BL/6 mouse used as control. 1781 of these 'shared' variants were present on the chromosome with the targeted Ackr4 allele (Chr9) and predominantly in close proximity to the Ackr4 locus, indicating that these variants originate from the 129-genetic background which was used for targeted mutagenesis during the generation of these mice. Conclusions: Our study shows that Ackr4-/- mice in generation F12 after backcrossing to the C57BL/6 background are still congenic for 129-derived DNA around the targeted Ackr4 locus, indicating that passenger mutations can influence the phenotype of these mice.
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Project description:The atypical chemokine receptor 4 (ACKR4)-expressing spleen endothelial cells (ECs) form a three-dimensional sinusoidal network connected via shunts to the marginal sinus and tightly surrounds the outer perimeter of the marginal zone. To better define this new vascular compartment within the red pulp of the spleen, were sorted CD31+ACKR4+ and CD31+ACKR4- EC populations, routinely yielding 92-98% cell purity and analyzed their transcriptional profiles.
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Project description:Purpose:Atypical classical chemokine receptor 4 (ACKR4) is a newly reported atypical classical chemokine receptor. However, its expression and role in MI are still unknown. This study aims to determine whether ACKR4 modulates cardiac remodeling following MI and to explore the specific molecular mechanism. Methods: RNA sequencing of infarcted hearts from WT and ACKR4-KO mice was performed at day 14 post-MI. Results: We generated a library of distinct transcriptome expression patterns.The consistency in the clustering suggested a homogeneous genomic activity with limited background signal and high levels of reproducibility across the three biological replicates in each group.Utilizing a P value < 0.05 and fold changes of 1.5 or greater, we identified 774 genes that are differentially expressed in ACKR4-KO mice compared to WT mice.The downregulated-genes belonged to the GO classes taxis, chemotaxis, extracellular matrix, and cytokine activity. Conclusions: These data provide the first insight into the role and mechanism of ACKR4 in MI.
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Project description:Gene expression analysis of in vitro activated B cells from C57BL/6 and Ackr4-deficient mice
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Project description:Exome Sequencing of Ackr4-deficient mice in generation 12 (backcrossing to C57BL/6)
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