201- Snap frozen cancer tissue and adjacent nonneoplastic tissues
from patients with esophageal adenocarcinoma. - 100% undenatured ethanol.
- DNase-free water.
- Micropipettes (10, 20, 200, and 1000 μL).
- DNase-free filtered tips (10, 20, 200, and 1000 μL).
- Microcentrifuge tubes.
- Microscope slides with a cover slip.
- Hematoxylin and eosin (H&E) staining reagents and
holders. - Microscope.
- Cryotome machine and relevant consumables (blades, cryo-
cassettes, etc.). - Microcentrifuge machine.
- Vortexer.
- Nanospectrophotometer (e.g., NanoDrop spectrophotometer).
- DNA extraction kit (e.g., Tissue and blood extraction kit from
Qiagen). - DNase-free water.
- Micropipettes (10, 20, 200, and 1000 μL).
- DNase-free filtered tips (10, 20, 200, and 1000 μL).
- Electrophoresis gel tank system and agarose gel caster with
well combs. - 1× Tris-acetate-EDTA (TAE) buffer.
- 10× loading dye.
- 100 bp DNA ladder.
- DNase-free water.
- 5% agarose gel.
- Microcentrifuge tubes.
- Polymerase chain reaction (PCR) tubes.
- 96-Well PCR plates.
- Pierceable foil heat seal.
- Primers.
- ddPCR supermix (e.g., Bio-Rad ddPCR™ Supermix for
Probes). - Restriction enzyme.
- PCR hood.
- Conventional PCR machine with gradient enabled function.
2.1 Tissue Collection
and DNA Extraction
2.2 ddPCR Primer
Optimization
DNA Copy-Number in Esophageal Adenocarcinoma