NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4100715 Query DataSets for GSM4100715
Status Public on Dec 21, 2019
Title ACKR4ko 1 Tail
Sample type SRA
 
Source name Tail
Organism Mus musculus
Characteristics tissue: tail
genotype: Ackr4-/- F12
gender: male
Growth protocol Mice were bred in the Central Animal Facility of the Hannover Medical School, Germany under SPF conditions, controlled day-night cycles and with food and water ad libidum.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from tail tissue was isolated with QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). DNA amount and purity was determined with Qubit dsDNA BR Assay Kit (Thermo Fischer Scientific).
1 µg DNA was used for library preparation with Agilent SureSelect XT Mouse All Exon Kit.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description common_S550Nr1_S550Nr2.vcf
unique_S550Nr2_vars.annotated.vcf
Data processing Library strategy: DNA-seq
demultiplexing (Illumina bcl2fastq 2.19)
adapter trimming (Skewer, 0.2.2)
alignment to the murine reference genome (mm10) with Burrows-Wheeler Aligner (BWA-mem 0.7.2-cegat), Reads aligned to multiple sides with the same mapping score were discarded
duplicate removal with with SAMtool 0.1.18
Genetic variants were identified with Verscan 2.4.2-cegat (26) and variants with a frequency of ≥ 2% were annotated with SnpEff (version 4.2 with GRCm38.75 )
Genome_build: mm10
Supplementary_files_format_and_content: VCF files contain the information on which position the samples deviate from the reference genome mm10. Point mutations are listed in the snps files and and insertions/deletions in the indels files. Annotated variant lists are in the files named with .annotated. Comparisions between WT (S550Nr1) and Ackr4-/- samples (S550Nr2 and S550Nr3) are labelled with common_ for the shared variants or with unique_ for the variants found in only one sample.
 
Submission date Sep 27, 2019
Last update date Dec 23, 2019
Contact name Nadine Eckert
E-mail(s) nadine.eckert89@web.de
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
 
Platform ID GPL24247
Series (1)
GSE138124 Exome Sequencing of Ackr4-deficient mice in generation 12 (backcrossing to C57BL/6)
Relations
BioSample SAMN12867744
SRA SRX6917580

Supplementary file Size Download File type/resource
GSM4100715_S550Nr2_indels.annotated.vcf.gz 187.4 Kb (ftp)(http) VCF
GSM4100715_S550Nr2_snps.annotated.vcf.gz 1.5 Mb (ftp)(http) VCF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap