Table 5 SIRO elements
From: Using semantics for representing experimental protocols
| Sample | Whole organism | Scientific name: Arabidopsis |
| thaliana, Oriza sativa, mangifera | ||
| indica, Mus musculus. | ||
| Common names: Mousear Cress, | ||
| rice, mango, mouse. | ||
| Anatomical part | Leaf, stem, cells, tissues, | |
| membranes, organs, skeletal | ||
| system, muscular system, | ||
| nervous system, reproductive | ||
| system, cardiovascular system, etc. | ||
| Biomolecules | Nucleic acids: Deoxyribonucleic acid | |
| (DNA) and ribonucleic acid (RNA). | ||
| Proteins: enzymes, structural or | ||
| support proteins (keratin, elastin, | ||
| collagen), antibodies, hormones, etc. | ||
| Body fluids | Blood serum, saliva, semen, amniotic | |
| fluid, cerebrospinal fluid, gastric | ||
| acid, etc. | ||
| Instrument | High-throughput | Liquid Handling Platforms, Real-Time |
| equipment | PCR Detection System, Microplate | |
| Reader, etc. | ||
| Instruments | Goggles, Bunsen burner, spot plate, | |
| pipet, forceps, test tube rack, mortar | ||
| and pestle, etc. | ||
| Laboratory glassware | Beaker, Erlenmeyer flask, graduated | |
| cylinder, volumetric flask, etc. | ||
| Standard equipment | Balances, shakers, centrifuges, | |
| refrigerators, incubators, | ||
| thermocyclers, fume hood, etc. | ||
| Consumables | Weighing dishes, pipette tips, gloves, | |
| syringes, petri dishes, test tubes, | ||
| micro centrifuge tubes, glass slides, | ||
| filter paper, etc. | ||
| Reagents | Chemical | Glucose, ethanol, glycerol, chloroform, |
| compound/Substance | acetic acid, isopropyl alcohol, etc. | |
| Solutions/buffers | 70% ethanol, 10X PCR buffer, | |
| phenol:chloroform:isoamyl | ||
| alcohol, etc. | ||
| Cell culture media | Nutrient media, minimal media, | |
| selective media, differential media, etc. | ||
| Objective | Part of discourse | Here we present a detailed protocol |
| for Smart-seq2 that allows the | ||
| generation of full-length cDNA and | ||
| sequencing libraries by using | ||
| standard reagents |