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| Status |
Public on Dec 21, 2019 |
| Title |
Exome Sequencing of Ackr4-deficient mice in generation 12 (backcrossing to C57BL/6) |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
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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| Overall design |
Genomic DNA from tail tissue of two Ackr4-deficient mice F12 and one C57BL/6 was compared by exome sequencing
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| Contributor(s) |
Eckert N, Förster R |
| Citation(s) |
31841228 |
| Submission date |
Sep 27, 2019 |
| Last update date |
Dec 23, 2019 |
| Contact name |
Nadine Eckert |
| E-mail(s) |
nadine.eckert89@web.de
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| Organization name |
Hannover Medical School
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| Department |
Immunology
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| Lab |
Förster
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| Street address |
Carl-Neuberg-Straße 1
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| City |
Hannover |
| State/province |
Lower Saxony |
| ZIP/Postal code |
30625 |
| Country |
Germany |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA574668 |
| SRA |
SRP223541 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE138124_RAW.tar |
4.7 Mb |
(http)(custom) |
TAR (of VCF) |
| GSE138124_common_S550Nr1_S550Nr2.vcf.gz |
45.3 Kb |
(ftp)(http) |
VCF |
| GSE138124_common_S550Nr1_S550Nr3.vcf.gz |
40.7 Kb |
(ftp)(http) |
VCF |
| GSE138124_unique_S550Nr1-2_vars.annotated.vcf.gz |
1.1 Mb |
(ftp)(http) |
VCF |
| GSE138124_unique_S550Nr1-3_vars.annotated.vcf.gz |
1.2 Mb |
(ftp)(http) |
VCF |
| GSE138124_unique_S550Nr2_vars.annotated.vcf.gz |
1.1 Mb |
(ftp)(http) |
VCF |
| GSE138124_unique_S550Nr3_vars.annotated.vcf.gz |
803.6 Kb |
(ftp)(http) |
VCF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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