|
| Status |
Public on Mar 12, 2021 |
| Title |
21662 neurocase |
| Sample type |
SRA |
| |
|
| Source name |
21662 neurocase
|
| Organism |
Canis lupus familiaris |
| Characteristics |
breed: Markiesje
diagnosis: juvenile paroxysmal dyskinesia
tissue: whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from EDTA blood samples using a Chemagic MSM1 robot (Perkin Elmer).
TruSeq Nano DNA HT Sample Prep Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
21662-NEUROCASE-POOL1
neuroCC.vcf
|
| Data processing |
Library strategy: DNA-Seq
Mapping with BWA (-c –l 25 -k 2 -n 10).
Variant calling was done using a custom pipeline identifying variants with at least 10x coverage, a 15% allele frequency as well as support from independent reads (>3).
Minimum sample call rate 80%.
Minimum depth 6x.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: neuroCC.vcf
|
| |
|
| Submission date |
Feb 12, 2021 |
| Last update date |
Mar 12, 2021 |
| Contact name |
Frank van Steenbeek |
| E-mail(s) |
f.g.vansteenbeek@uu.nl
|
| Phone |
0302532848
|
| Organization name |
Utrecht University
|
| Street address |
Yalelaan 104
|
| City |
Utrecht |
| State/province |
Select State/Province |
| ZIP/Postal code |
3584 CM |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL22370 |
| Series (1) |
| GSE166712 |
A knockout mutation associated with juvenile paroxysmal dyskinesia in Markiesje dogs indicates SOD1 pleiotropy |
|
| Relations |
| BioSample |
SAMN17900871 |
| SRA |
SRX10089551 |
