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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