|
| Status |
Public on Jan 13, 2022 |
| Title |
[Standard curve] Input WT 1% #3 |
| Sample type |
SRA |
| |
|
| Source name |
Plasmid PCR fragment
|
| Organism |
Escherichia coli |
| Characteristics |
sample type: Plasmid
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
A 4 or 5 mm punch biopsy was performed on a patient's clinically revertant skin spots that did not show any skin fragility via manual rubbing. Adjacent non-revertant skin samples were also obtained.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted from the epidermis, dermis, or peripheral blood by the Puregene Blood Core Kit (Qiagen, Valencia, CA, USA).
Libraries were constructed using Ligation Sequencing Kit SQK-LSK109 and Native Barcoding Expansion kit EXP-NBD104 and EXP-NBD114 (Oxford Nanopore Technologies). gDNA was treated with Quick Calf Intestinal Phosphatase and Cas9 before library construction for Nanopore Cas9-targeted sequencing (nCATS).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Description |
DNA-seq
plasmid DNA
1_standard_curve_counts.txt
|
| Data processing |
Basecalls were performed using Guppy 5.0.11 using dna_r9.4.1_450bps_sup.cfg as a DNA model.
Mapping to the genomic sequence of COL7A1 (RefSeq Accession # NC_000003.12:c48595302-48564073) using minimap2 2.16-r922.
Information of reads mapped to both loci of the mutations (19630th base of the reference for c.5932C>T, 27712th base for c.8029G>A) was extracted using samtools.
Supplementary_files_format_and_content: Count of haplotype of each read.
|
| |
|
| Submission date |
Oct 15, 2021 |
| Last update date |
Jan 13, 2022 |
| Contact name |
Yoshikazu Furuta |
| E-mail(s) |
yfuruta@czc.hokudai.ac.jp
|
| Organization name |
Hokkaido University
|
| Department |
International Institute for Zoonosis Control
|
| Lab |
Division of Infection and Immunity
|
| Street address |
North 20 West 10, Kita-ku
|
| City |
Sapporo |
| State/province |
Hokkaido |
| ZIP/Postal code |
001-0020 |
| Country |
Japan |
| |
|
| Platform ID |
GPL30119 |
| Series (1) |
| GSE186002 |
Detection of revertant mosaicism in epidermolysis bullosa through Cas9-targeted long read sequencing |
|
| Relations |
| BioSample |
SAMN22328921 |
| SRA |
SRX12633426 |
