|
| Status |
Public on Jul 31, 2019 |
| Title |
Dux-KO_ mixture of liver and muscles |
| Sample type |
SRA |
| |
|
| Source name |
organs genome
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Dux KO
tissue: mixture of liver and muscles
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High quality genome DNA was extracted from organs of Dux knockout mouse according to the standard protocol by phenol:chloroform extraction and ethanol precipitation.
Genome DNA library was prepared for sequencing using standard PacBio Sequel protocol
Third-generation whole-genome sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Sequel |
| |
|
| Description |
whole genome
|
| Data processing |
Library strategy: DNA-Seq
The PacBio reads were aligned to the mouse genome (mm9) using pbmm2 (version 1.0.0), a wrapper of minimap2 with deault settings.
We used variantCaller (version 2.3.3 ) to get the consensus and variant calling using the algorithm “arrow”.
The positions with read coverage less than 5 were marked by Ns in the consensus sequence.
Genome_build: mm9
Supplementary_files_format_and_content: genomic consensus sequence of knockout Dux gene and its vicinity (30 kb upstream and 30kb downstream ), fasta format
|
| |
|
| Submission date |
Jul 25, 2019 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Mingyue Guo |
| E-mail(s) |
1610815@tongji.edu.cn
|
| Phone |
86-21-65982278
|
| Organization name |
Tongji University
|
| Department |
School of Life science and technology
|
| Lab |
Gao Shaorong
|
| Street address |
Siping
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL24198 |
| Series (2) |
| GSE134830 |
Third-generation long-read whole-genome sequencing of Dux knockout mouse |
| GSE134832 |
Precise temporal regulation of Dux is important for embryo development |
|
| Relations |
| BioSample |
SAMN12360786 |
| SRA |
SRX6587859 |
