Computational protocol: RHBDD1 promotes colorectal cancer metastasis through the Wnt signaling pathway and its downstream target ZEB1

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Protocol publication

[…] The RNA sequencing was performed in triplicate in each group. Total RNA was isolated from HCT-116 cells transfected with either Si-RHBDD1-pool or Control Si-RNA. The isolated RNAs were subjected to quality control, mRNA library establishment and Illumina HiSeq sequencing. HTSeq software was used to get the gene expression levels. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Genes with a padj< 0.05 found by DESeq were assigned as differentially expressed. The KEGG pathway enrichment analysis result is shown as the adjusted P value (padj), differential gene count and gene ratio (differential gene count in this pathway versus total differential gene count). A heatmap analysis is shown as normalized gene expression (FPKM). […]

Pipeline specifications

Software tools HTSeq, DESeq
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Colonic Neoplasms, Myositis Ossificans, Neoplasms, Colorectal Neoplasms