cell type: GI tract mixed cells (not microdissected)
Extracted molecule
genomic DNA
Extraction protocol
QIAamp® DNA FFPE Tissue Kit (Qiagen, Valencia, CA, USA) for manual microdissection samples and PicoPure® DNA Extraction Kit (Arcturus Bioscience, Mountain View, CA, USA) for laser microdissection samples, respectively, in accordance with the manufacturer's protocol.
Label
Cy5
Label protocol
Genomic DNA ULS Labeling Kit (Agilent Technologies) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) Protocol; Version 3.1, August 2009; Manual Part Number G4410-90020
QIAamp® DNA FFPE Tissue Kit (Qiagen, Valencia, CA, USA) for manual microdissection samples and PicoPure® DNA Extraction Kit (Arcturus Bioscience, Mountain View, CA, USA) for laser microdissection samples, respectively, in accordance with the manufacturer's protocol.
Label
Cy3
Label protocol
Genomic DNA ULS Labeling Kit (Agilent Technologies) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) Protocol; Version 3.1, August 2009; Manual Part Number G4410-90020
Hybridization protocol
Agilent Oligo aCGH Hybridization Kit (p/n 5188-5220) and Agilent Oligo aCGH Wash Buffers (p/n 5188-5226) were used according to manufacturer protocols.
Scan protocol
Agilent G2565BA Scanner was used according to manufacturer protocol. Data extraction has been performed with Agilent G2567AA Feature Extraction Software v10.5.1.1.
Data processing
Feature extraction data was obtained using Agilent G2567AA Feature Extraction Software (v10.5.1.1), normalized using LOcally-WEighted regression Scatterplot Smoother
Array comparative genomic hybridization (aCGH) study of formalin-fixed paraffin-embedded (FFPE) small gastrointestinal stromal tumors (GISTs) less than 1 cm in greatest diameter (microGISTs)
Data table header descriptions
ID_REF
VALUE
Normalized log2 ratio (Cy5/Cy3) representing test/reference (Ref.: Protopopov A, Feng B, Chin L. Full Complexity Genomic Hybridization on 60-mer Oligonucleotide Microarrays for Array Comparative Genomic Hybridization (aCGH). Methods Mol Biol. 2008;439:87-100)
