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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: 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

PROVIDER: PRJNA631772 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11772854.fastq.gz	Fastqsanger.gz
	SRR11772855.fastq.gz	Fastqsanger.gz
	SRR11772856.fastq.gz	Fastqsanger.gz
	SRR11772857.fastq.gz	Fastqsanger.gz
	SRR11772858.fastq.gz	Fastqsanger.gz

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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

Project description: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.

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Project description: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, immune deficienct, tumor and immune deficient tumor condition and using a Drosophila inducible intestinal tumor model to identify signaling cascades that involved in tumorigenesis downstream of immune signaling pathway Methods: intestine mRNA profiles of 7-day old control (esgts>w1118), immune deficient (esgts>RelishE20), Shn-RNAi (esgts>Shn-RNAi_KK) and Shn-RNAi plus immune deficient (esgts>Shn-RNAi,RelishE20) Drosophila were generated by deep sequencing, Shn-RNAi in triplicate, Control, and RelishE20 or Shn-RNAi plus RelishE20 in duplicate, using Illumina GAIIx. Results: Using an optimized data analysis workflow, we mapped about 21 million sequence reads per sample to the Drosophila genome (ENSEMBL BDGP6.22) and identified a total of 146,391 million counts in the Drosophila midgut of control, immune deficienct, tumor and immune deficient tumor condition. 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 intestinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The data analysis revealled that pro-apoptotic gene signature is governed by immune signaling pathway that are required for intestinal tumorigenesis in Drosophila

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