Protocol 4B: PANAMAX 48 extraction of tissue genomic DNA
Instrument role
For tissue, PANAMAX 48 automates a kit-specific magnetic-bead bind–wash–elute workflow after appropriate tissue lysis. The target is purified genomic DNA suitable for controlled fragmentation and EM-seq.
| Input | Physical output | Data recorded now | Data generated later |
|---|---|---|---|
| prepared colonic tissue lysate | genomic-DNA eluate | run, kit/lot, well, volumes, flags | fragment profile, library metrics, CpG counts |
The study must record the exact PANAMAX tissue/genomic-DNA kit, catalogue number, lysis conditions, input limits, program/software version, and elution settings. They cannot be reconstructed safely from “PANAMAX 48” alone.
QC gate
Quantify yield with a DNA-appropriate fluorometric assay, assess integrity/fragment profile, document purity and inhibitors, retain extraction blanks, and check replicate consistency. High DNA yield does not guarantee an unbiased methylome.
The output is DNA, not tabular biological data. The first derived distribution is created by UltraShear and fragment analysis; base-level methylation arrives after sequencing and alignment.
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