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Exome Sequencing of Ackr4-deficient mice in generation 12 (backcrossing to C57BL/6)

ABSTRACT: Exome Sequencing of Ackr4-deficient mice in generation 12 (backcrossing to C57BL/6)

PROVIDER: PRJNA574668 | ENA |

REPOSITORIES: ENA

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Exome Sequencing of Ackr4-deficient mice in generation 12 (backcrossing to C57BL/6)

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.

2019-12-21 | GSE138124 | GEO

ATAC-seq analysis of murine thymic iNKT subsets from C57BL/6 mice and Hivep3-deficient mice

Project description:ATAC-seq analysis of murine thymic iNKT subsets from two independent C57BL/6 mice and two independent Hivep3-deficient mice

2020-10-31 | GSE160518 | GEO

Mouse spleen LC-MSMS from C57BL/6J WT, CD38-deficient and B6.C-H2bm12/KHEg (bm12) mice in cGVHD lupus-like model

Project description:Proteins from post-nuclear cell lysates from C57BL/6J WT, CD38-deficient and B6.C-H2bm12/KHEg (bm12) recipient mice at 2 weeks after the adoptive transfer of co-isogenic spleen cells were identified using a proteomic approach. The relative abundances of the proteins identified were calculated using emPAIs scores.

2021-10-11 | PXD026947 | Pride

Transcriptome of CD8+T-cells from C57BL/6 mice in induced tumor-like conditions along with IL-2 and IL-12.

Project description:To study differentially expressed genes via RNA seq analysis of CD8+T-cells from C57BL/6 mice splenocytes treated with the four different conditions: IL-2, IL-2 80%TCM, IL-12 and IL-12 80%TCM. (TCM = Tumor Conditioned Media)

2021-11-23 | GSE189170 | GEO

Gene expression analysis of in vitro activated B cells from C57BL/6 and Ackr4-deficient mice

Project description:To further understand differential phenotypes between C57BL/6 and Ackr4-deficient B cells, we have employed whole genome microarray expression profiling as a discovery platform to identify genes which are differentially expressed in the two genotypes. Murine B cells from spleens of C57BL/6 and Ackr4-deficient mice were purified by negative magnetic activated cell sorting (MACS) and activated in vitro with 10 µg/mL polyclonal anti-IgM and10 µg/mL anti-CD40 (clone FGK4.5) antibodies for three days in culture (96well plate, 37°C, 5%CO2). On day three, living B cells were sorted and RNA was extracted.

2019-12-21 | GSE138175 | GEO

Expression data of primary melanocytes from aryl hydrocarbon deficient mice and corresponding wild-type C57BL/6 mice

Project description:[original Title] Comparison of expression data of primary murine melanocytes from aryl hydrocarbon deficient mice and corresponding wild-type C57BL/6 mice Melanin is produced exclusively by melanocytes and melanogenesis is the vital response to protect skin cells against Ultraviolet B (UVB)-induced DNA damage. The aryl hydrocarbon receptor (AhR) is a transcription factor, which may be involved in the physiological tanning response. Normal murine melanocytes express functional AhR. We tested gene expression in WT versus AhR-deficient mice primary murine melanocytes, isolated from the skin and cultivated for several passages. Skin epidermal cells from 2 individual C57BL/6 mice and 2 individual AhR-deficient mice (deletion of exon2, AhRtm1Bra) were grown for 6-8 weeks in selection medium to propagate melanocytes.

2010-09-05 | E-GEOD-19411 | biostudies-arrayexpress

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

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

| PRJNA644722 | ENA

Generation and characterization of thiol-deficient Mycobacterium tuberculosis mutants

Project description:Mycothiol (MSH) and ergothioneine (ERG) are thiols able to compensate for each other to protect mycobacteria such as Mycobacterium smegmatis against oxidative stress. Gamma-glutamylcysteine (GGC), another thiol and an intermediate in ERG biosynthesis has detoxification abilities. Five enzymes are involved in ERG biosynthesis, namely EgtA, EgtB, EgtC, EgtD and EgtE. The role of these enzymes in the production of ERG had been unclear. On the other hand, the enzyme MshA is known to be essential for MSH biosynthesis. In this manuscript, we describe the raw data of the generation and characterization of Mycobacterium tuberculosis (M.tb) mutants harbouring a deletion of the gene coding for each of these enzymes, and the raw data of the phenotypic characterization of the obtained thiol-deficient M.tb mutants. Through a high throughput screening approach, compounds not previously used in a tuberculosis (TB) regimen were identified. Raw data depicting the effect of these compounds on the generated thiol-deficient M.tb mutants, on the production of reactive oxygen species (ROS) and thiols in the M.tb wild type strain are described in this study.

2018-07-05 | MTBLS661 | MetaboLights

Expression data of primary melanocytes from aryl hydrocarbon deficient mice and corresponding wild-type C57BL/6 mice

2010-09-05 | GSE19411 | GEO

Transcription profiling of livers of C57BL/6 mice and LDL receptor deficient mice fed on either low fat or high fat diet to study liver gene expression associated with diet.

Project description:Examination of gene expression profiles from liver of C57BL/6 mice and LDL receptor deficient mice fed on either a low fat diet or a high fat Western-style diet for 12 weeks. Three replicates of each condition analyzed. Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver

2007-11-01 | E-GEOD-363 | biostudies-arrayexpress

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