Table 3 Procedures and subprocedures from “Extraction of total RNA from fresh/frozen tissue (FT)”
From: Using semantics for representing experimental protocols
| Procedure | Subprocedure |
|---|---|
| Protocol overview (sp:lab procedure 1) | Recover tumor tissue at the time of surgery, trim into 1-cm3 fragments, and immerse immediately in TRIzol reagent prior to freezing at −80°. |
| Thaw and weigh tissue prior to RNA extraction, working quickly. | |
| Use a tissue power homogenizer (or a mortar and pestle) to homogenize tissue by hand. | |
| Prior to RNA extraction: cleaning process of equipment (sp:lab procedure 2) | Autoclave or wash equipment (i.e., tissue storage container, homogenizer blades, forceps, scalpel holder) in Neutracon solution for 2–4 h. |
| Rinse equipment well in 1% SDS (prepared using DEPC-treated or other nuclease-free water). | |
| Rinse in 100% ethanol and leave to air-dry. | |
| RNA extraction (sp:lab procedure 3) | Homogenize sample using tissue homogenizer. |
| Add 0.2 mL chloroform per 1 mL TRIzol and cap tube tightly. | |
| Add 0.5 mL isopropyl alcohol per 1 mL TRIzol. | |
| Add 1 mL 75% ethanol per 1 mL TRIzol and vortex for 10 s. |