|
| Status |
Public on Apr 20, 2024 |
| Title |
MAP8.B6.Ly49m_KO_nanopore |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: Splenocytes
genotype: MAP8.B6.Ly49m_KO
treatment: NA
|
| Treatment protocol |
Total splenocytes were isolated from mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High molecular weight DNA was extracted from ~5 million splenocytes of 1 MAP8.B6.Ly49h or MAP8.B6.Ly49m KO mouse, using Gentra Puregene Cell Kit (8 x 10^8) (catalog # 158767).
8 ug of DNA was then fragmented using Covaris g-TUBE (catalog 520079), which was spun at 4200 rpm to fragment the DNA to an average size of 50 Kb. The 7.7 ug DNA recovered after fragmentation was subsequently cleaned using Short Fragment Eliminator (Oxford Nanopore EXP-SFE001). The sequencing library was prepared using Ligation Sequencing Kit V14 (ONT SQK-LSK114) with 2 ug DNA as input, and 22 fmol of the library was run on a single PromethION flow cell (FLO-PRO114M) for 42 hours without reloading.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Data processing |
Base-calling from raw sequencing data was perform using Guppy (v6.4.6) with the dna_r10.4.1_e8.2_400bps_sup model. Base-called reads (fastq file) were aligned to the mouse genome (mm10) using minimap2 (v2.24, -ax map-ont).
We then filtered the fastq file for reads mapped to the Ly49 locus (chr6:129800001-130500000), irrespective of their mapping status (primary, secondary, or supplementary). These reads were used to perform de novo assembly of the Ly49 locus using flye (v2.9.2, --nano-hq -g 700k).
Assembly: mm10
Supplementary files format and content: fa: assembled Ly49 locus
Library strategy: DNA-Seq
|
| |
|
| Submission date |
Feb 16, 2024 |
| Last update date |
Apr 20, 2024 |
| Contact name |
Changxu Fan |
| E-mail(s) |
fanc@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue, Room 5213
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL26624 |
| Series (2) |
| GSE226502 |
Epigenetic evolution of the Ly49 gene family |
| GSE233982 |
Epigenetic evolution of the Ly49 gene family [NanoPore] |
|
| Relations |
| BioSample |
SAMN39969362 |
| SRA |
SRX23645981 |
