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Series GSE138124 Query DataSets for GSE138124
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
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.
Overall design Genomic DNA from tail tissue of two Ackr4-deficient mice F12 and one C57BL/6 was compared by exome sequencing
Contributor(s) Eckert N, Förster R
Citation(s) 31841228
Submission date Sep 27, 2019
Last update date Dec 23, 2019
Contact name Nadine Eckert
Organization name Hannover Medical School
Department Immunology
Lab Förster
Street address Carl-Neuberg-Straße 1
City Hannover
State/province Lower Saxony
ZIP/Postal code 30625
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (3)
GSM4100714 WT tail
GSM4100715 ACKR4ko 1 Tail
GSM4100716 ACKR4ko 2 Tail
BioProject PRJNA574668
SRA SRP223541

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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
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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