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The main principle is the following: By modeling the actual research domain in the form of a domain ontology (Step 1 of the process), the domain-experts build the base for all subsequent steps.
A high-salt (2.7%) Tris-buffered saline containing 0.3% Triton-X (TBS/TX) was used for all subsequent steps.
This enabled all samples to be combined for all subsequent steps of RAD library preparation and sequencing.
5 d old light-grown uniformly germinated seedlings were washed seven times with sterile water with last wash given by 1/2MS liquid medium to remove residual exogenous sugar and the plant material was kept in 1/2MS liquid without sucrose in the dark for all subsequent steps.
Singletons (i.e. unassembled reads) were discarded for all subsequent steps.
Hearts and testes were placed on the same coverslip for all subsequent steps.
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For selecting individual soluble scFvs, the detergent was omitted from the diluent for this and all subsequent steps.
Five in vitro transcribed bacterial RNAs were spiked into each of the fractions at equivalent amounts and were used to normalize for differences in all subsequent steps of the procedure, including RNA purification, labeling with fluorescent dyes, hybridization to DNA microarrays and scanning [ 19].
For direct comparison, affinity and control matrices were combined for protein elution and all subsequent steps, including separation by 1D SDS-PAGE (to reduce complexity) and identification of eluted proteins by mass spectrometry.
The sections were then cooled to room temperature for 20 minutes and all subsequent steps carried out at room temperature.
Five μg of total RNA were incubated with oligo-dT primer and 1 μl PNA master mix for 10 minutes at 70°C prior to first strand cDNA synthesis; all subsequent steps for target amplification and labeling were as described for Method 1. Globin mRNA depletion was performed in three steps using the GLOBINclear Kit (Ambion, Austin, TX, USA).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com