|
| Status |
Public on Dec 21, 2019 |
| Title |
WT tail |
| Sample type |
SRA |
| |
|
| Source name |
Tail
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tail
genotype: C57BL/6
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 |
unique_S550Nr1-2_vars.annotated.vcf
unique_S550Nr1-3_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 |
SAMN12867745 |
| SRA |
SRX6917579 |
