Next Generation Sequencing Analysis of Wild Type intestine(Control), intestine with tumor (Shn-RNAi ) and intestine with severe tumor (Shn-RNAi plus Puc mutation) Transcriptomes

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived intestinal transcriptome profiling between control, tumor and severe tumor condition and using a Drosophila inducible intestinal tumor model to identify signaling cascades involved in tumorigenesis Methods: intestine mRNA profiles of 7-day old control (esgts>w1118), Shn-RNAi (esgts>Shn-RNAi_KK) and Shn-RNAi plus Puc mutaion (esgts>Shn-RNAi,PucE69/+) Drosophila were generated by deep sequencing, Control in triplicate, and Shn-RNAi or Shno-RNAi in duplicate, using Illumina GAIIx. Results: Using an optimized data analysis workflow, we mapped about 19 million sequence reads per sample to the Drosophila genome (ENSEMBL BDGP6.22) and identified a total of 105,674 million counts in the midgut of control, Shn-RNAi and Shn-RNAi plus puc mutation Drosophila. Salmon was used to map and quantify the transcript abundance and DESeq2 was used for the gene expression analysis. DAVID GO term analysis for biological processes clustering of differentially expressed genes enriched for certain known pathays. Conclusions: Our study represents the detailed analysis of Drosophila intestinal transcriptomes with control and 2 tumor conditions, with biologic replicates, generated by RNA-seq technology. The data analysis showed that signaling pathways are enriched in tumor conditions such as EGFR, NFkB, JAK/STAT and JNK.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE150328 | GEO | 2021/06/30

REPOSITORIES: GEO