Computational protocol: JIB-04, A Small Molecule Histone Demethylase Inhibitor, Selectively Targets Colorectal Cancer Stem Cells by Inhibiting the Wnt/β-Catenin Signaling Pathway

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Protocol publication

[…] The RNA sequencing was processed by Macrogen, Inc. (Seoul, South Korea). RNA extracts from cells treated with DMSO or 2 µM JIB-04 for 24 h were subjected to cDNA library construction (TruSeq RNA Sample Prep Kit v2). The sample was checked for quality using FastQC v0.10.0 and then subjected to Illumina sequencing using the HiSeq. 4000 system. We aligned the sequencing reads to the reference genome using TopHat version 2.0.13 and bowtie2 2.2.3. We used Cufflinks version 2.2.1 to detect differences in expression between samples. We used the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to determine the pathways of the differentially expressed genes. We selected significant pathways using Fisher’s exact test with the threshold of significance set by P-value and False Discovery Rate (FDR). The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE106407 ( […]

Pipeline specifications

Software tools FastQC, TopHat, Bowtie2, Cufflinks
Databases GEO KEGG
Application RNA-seq analysis
Diseases Neoplasms, Colorectal Neoplasms