Human cell line DNA – QIAGEN Genomic-tip
Oxford Nanopore
Human cell line DNA – QIAGEN Genomic-tip
FOR RESEARCH USE ONLY
Contents
Materials
Method
Results
Sequencing performance
Materials
- Cell culture
- Qiagen Blood and Cell Culture DNA Maxi Kit
- 70% ethanol in nuclease-free water
- TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0)
- 50 ml Falcon tubes
- Shaker for Eppendorf tubes
- Microfuge
Method
Harvest 1 x 10^8 cells and lyse them according to the QIAGEN Genomic DNA Handbook from the Preparation of cell culture section on page 25.
Follow the QIAGEN Genomic-tip handbook, starting on the Isolation of genomic DNA from blood, cultured cells, tissue, yeast, or bacteria using genomic-tips secton on page 49.
Optional Step: At the elution stage, use buffer QF warmed up to 50°C, and spin down the precipitated DNA at 4300 g for 15 minutes at 4°C. Wash the pellet with cold 70% ethanol, and spin down at 4400 g for 10 minutes at 4°C.
Resuspend the pellet in 1 ml of sterile TE (10 mM Tris-HCl 1 mM EDTA, pH 8.0) on a platform shaker overnight at room temperature.
Results
- Yield: 400-450 ng/µl
- OD 260/280: 1.9
- OD 260/230: 2.4
- Fragment size (FEMTO pulse):
Sequencing performance
Libraries for Nanopore sequencing were prepared using the Ligation Sequencing Kit.
- Read length profile with and without g-TUBE fragmentation, and sequencing:
| Version | Change |
|---|---|
| v1, January 2022 | Initial protocol release |
| v2, June 2023 | Removed reference to specific kit codes |
| v3, August 2023 | Updated materials required and updated QIAGEN protocol name |