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Neoplastic tissue, less than 1 mm, was excised from each FFPE block to retrieve sections corresponding to KIT positive immunostaining areas.
The qualitative software computer package NUD*IST (QSR International Pty, Doncaster, Victoria, Australia) was used to store and retrieve sections of the data.
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Retrieved sections of the text were grouped according to content similarity.
It is composed of three sections, i.e., the searching section, the interaction retrieving section and the network analysis section.
To retrieve antigenicity, sections were immersed in antigen retrieval buffer, pH 9 (Dako, Carpinteria, CA), and heated for 20 min in a steam pressure cooker (Pascal, Dako).
Endogenous peroxidase activity was blocked by immersing sections in 0.3% H2O2 (Sigma, H1009) diluted in methanol for 30 min. To retrieve antigens, sections were boiled in 0.01 M citrate (pH 6.0) or 0.01 M EDTA buffer (pH 8.0).
MaxQDA software allowed systematic searches through data to retrieve relevant sections.
To retrieve antigenicity, sections were heated by autoclave in 10 mM citrate buffer for 20 min [ 28].
To retrieve antigenicity, sections were immersed in 500 ml (pH 6.0) citrate buffer and heated for 10 min in an 800 W microwave at high power, followed by 10 min at low power.
In any cases these sequences were obtained from RSAtools (retrieve sequence section, default parameters).
The nucleotide sequences in the vicinity of the start codon (from −100 to +24 and −30 to +24 relatives to ATG) were also obtained from RSAtools (retrieve sequence section, default parameters).
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