Computational protocol: Long noncoding RNA GAPLINC promotes invasion in colorectal cancer by targeting SNAI2 through binding with PSF and NONO

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Protocol publication

[…] Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Shanghai, China). The RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Labeled samples were hybridized to the Agilent Human 4×44K Gene Expression Microarrays v2 (KangChen Biotech, Shanghai, China). After washing, the microarray slides were scanned using an Agilent DNA microarray scanner. The array images were analyzed by the Agilent Feature Extraction Software (version 11.0.0.1, CA, USA). Then, further bioinformatics analyses were performed using the Agilent GeneSpring GX software (version 12.1, CA, USA). Finally, pathway analysis and Gene Ontology (GO) analysis were performed to determine the roles of differentially expressed genes in these biological pathways or GO terms. […]

Pipeline specifications

Software tools Agilent Feature Extraction, GeneSpring GX
Application Gene expression microarray analysis
Organisms Homo sapiens
Chemicals Zinc