Accession

PRJNA663474

Title

Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

Relevance

Medical

Data types

Transcriptome or Gene expression

Sample scope

Multiisolate

Organism

Homo sapiens [Taxonomy ID: 9606]

Description

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare TP53-WT and TP53-KO HCT116 cells transcriptome profiling (RNA-seq) under 5-FU treatment condition and to evaluate the correlation between transcriptome profileing and chromatin accessibility under 5-FU treatment. Methods: HCT116 cell profiles of TP53-WT and TP53- KO were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform levels: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). Conclusions: Our study represents the detailed analysis of TP53-WT and TP53-KO HCT116 cell transcriptomes under 5-FU treatment with different timepoint, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that RNA-seq offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a TP53-WT and TP53-KO cells with and without 5-FU treatment in different timepoint. We conclude that NGS based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: 5-FU treated and non-treated mRNA profiles of TP53-WT and TP53-KO cells in different timepoint.

Publication

PubMed ID	Article title	Journal name	DOI	Year
33613715

External link

Link description

Organization

Department of Tropical Medicine, Yonsei University College of Medicine

Data Source

NCBI

Project Data

Resource name	Description
Experiment (16) show	-
SRX9124068	GSM4781646: RNA-seq of p53 KO 5-FU 300um treated 24h rep1; Homo sapiens; RNA-Seq
SRX9124069	GSM4781647: RNA-seq of p53 KO 5-FU 300um treated 24h rep2; Homo sapiens; RNA-Seq
SRX9124072	GSM4781650: RNA-seq of p53 KO 5-FU 300um treated 30min rep1; Homo sapiens; RNA-Seq
SRX9124073	GSM4781651: RNA-seq of p53 KO 5-FU 300um treated 30min rep2; Homo sapiens; RNA-Seq
SRX9124074	GSM4781652: RNA-seq of p53 WT 5-FU non treated rep1; Homo sapiens; RNA-Seq
SRX9124075	GSM4781653: RNA-seq of p53 WT 5-FU non treated rep2; Homo sapiens; RNA-Seq
SRX9124070	GSM4781648: RNA-seq of p53 KO 5-FU 300um treated 2h rep1; Homo sapiens; RNA-Seq
SRX9124076	GSM4781654: RNA-seq of p53 WT 5-FU 300um treated 24h rep1; Homo sapiens; RNA-Seq
SRX9124077	GSM4781655: RNA-seq of p53 WT 5-FU 300um treated 24h rep2; Homo sapiens; RNA-Seq
SRX9124071	GSM4781649: RNA-seq of p53 KO 5-FU 300um treated 2h rep2; Homo sapiens; RNA-Seq
SRX9124079	GSM4781657: RNA-seq of p53 WT 5-FU 300um treated 2h rep2; Homo sapiens; RNA-Seq
SRX9124080	GSM4781658: RNA-seq of p53 WT 5-FU 300um treated 30min rep1; Homo sapiens; RNA-Seq
SRX9124078	GSM4781656: RNA-seq of p53 WT 5-FU 300um treated 2h rep1; Homo sapiens; RNA-Seq
SRX9124081	GSM4781659: RNA-seq of p53 WT 5-FU 300um treated 30min rep2; Homo sapiens; RNA-Seq
SRX9124066	GSM4781644: RNA-seq of p53 KO 5-FU non treated rep1; Homo sapiens; RNA-Seq
SRX9124067	GSM4781645: RNA-seq of p53 KO 5-FU non treated rep2; Homo sapiens; RNA-Seq