SW480 and SW480-HNF4 α OE RNA sequencing

Published: 10 September 2024| Version 1 | DOI: 10.17632/vn3s2wrmcx.1
Contributor:
Jianwei Sun

Description

The total RNA of SW480 and SW480-HNF4α cells were harvested with Trizol. Three biological replicates were used. These samples were subjected to transcriptome RNA-sequencing by Novogene. The paired-end RNA-sequencing library was employed (2 × 150 bp read length) using an Illumina NovaSeq 6000 sequencer.

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Steps to reproduce

he index construction is performed using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), the genome alignment of the clean data is conducted using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml), and the transcriptome assembly is performed using Cufflinks (https://cole-trapnell-lab.github.io/cufflinks/). The gene expression level was calculated according to the fragments per kilobase million reads (FPKM) method. The formula for differential analysis calculation is log2(SW480-HNF4α mean (FPKM)/SW480 control mean (FPKM)). The p-value is calculated using the t-test different expressed genes (DEGs) with |log2(foldchange)| ≥ 1, and P-value < 0.05 were considered to be significantly (DEGs).

Institutions

Yunnan University

Categories

Colorectal Cancer

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