Computational protocol: Transcriptome Reveals 1400-Fold Upregulation of APOA4-APOC3 and 1100-Fold Downregulation of GIF in the Patients with Polycythemia-Induced Gastric Injury

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Protocol publication

[…] Single-color gene-expression profiles were produced by comparing the expression-level difference between the experimental subjects and controls. These profiles were constructed by 4 × 44 K oligonucleotide microarrays from Agilent Technologies (Palo Alto, CA, USA). The mouse genome microarray covers about 41,000 genes and transcripts. The representative sequences were obtained from public databases, including RefSeq, Ensembl, Unigene, and UCSC Goldenpath. The RNA samples were amplified and labeled using the labeling kit from Agilent Technologies (Palo Alto, CA, USA) according to manufacturer instructions and hybridized with the Agilent mouse genome microarray in the hybridization chambers of Agilent’s SureHyb. After hybridization and washing, the hybridized slides were scanned by DNA microarray scanner (G2505B) and evaluated with the Agilent Feature Extraction Analytics software (version 9.5.3). The Feature Extraction placed microarray grids, rejected outlier pixels, determined feature intensities and ratios, flagged outlier pixels, and compiled QC reports. All the procedures were conducted by KangChen Bio-Tech, Shanghai, China. The Agilent GeneSpring GX software (version 7.3, Agilent Technologies, CA, USA) was used to calculate and record the signal intensities representing the gene expression levels generated by the Agilent 4 × 44 K One-Color Whole Genome Microarray. For inter-array normalization, a median normalization was used. For data analysis, fold changes were applied to select the differentially expressed genes (DEGs) using 2-fold change cutoff. Genes were regarded as up-regulated gene with 2-fold or higher expression compared to a control; genes were regarded as down-regulated genes with 2-fold lower expression, and 0.50- to 1.99-fold changes could be regarded as non-significant. Therefore, the profiling identified a subset of the total number of DEGs. […]

Pipeline specifications

Software tools Agilent Feature Extraction, GeneSpring GX
Application Gene expression microarray analysis
Organisms Homo sapiens
Diseases Anemia, Mouth Diseases, Polycythemia, Stomach Diseases, Stomach Neoplasms