Human cell line DNA – QIAGEN Genomic-tip

Materials

Method

  1. 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.

  2. 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.

  3. 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.

  4. 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

cell lines QIAGEN

  • Fragment size (FEMTO pulse):

Cell lines QIAGEN fragmentation

Sequencing performance

Libraries for Nanopore sequencing were prepared using the Ligation Sequencing Kit.

  • Read length profile with and without g-TUBE fragmentation, and sequencing:

Cell lines QIAGEN fragmentation 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

Last updated: 8/16/2023

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