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Next Generation Sequencing Facilitates Quantitative Analysis of control and AOM+DSS mouse model Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of control and AOM+DSS mouse model Transcriptomes

PROVIDER: PRJNA525853 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8690195.fastq.gz	Fastqsanger.gz
	SRR8690196.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of control and AOM+DSS mouse model Transcriptomes

Project description:The goal of this study is to screen the differential genes between control and AOM+DSS mouse model, then analyze the significant pathways.

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and RNF138-/- mice colorectal transcriptomes in DSS, AOM/DSS and organoids samples

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis NGS-derived transcriptome profiling (RNA-seq) in DSS induced chronic inflammation, AOM/DSS induced colitis-associated colorectal tumorigenesis and organoids isolation from colitis-associated colorectal tumorigenesis Methods: DSS, AOM/DSS and organoids mRNA profiles of wild-type (WT) and RING Finger 3 (RNF138−/−) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads were trimmed for low-quality sequence, then mapped to mm10 whole genome using STAR v2.6.1d Results: Using an optimized data analysis workflow, the padj <0.05 and fold change >2 were refered as differential expression. There are 987, 2649 and 2373 differential genes were found in RNF138-/- compared with Wild Type in DSS, AOM/DSS and organoids, respectively Conclusions: Our study revealed NFκB pathway is the main activation pathway regulated by RNF138 loss

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mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice --- miRNA microarray

Project description:To find out which miRNAs are significantly differential expression and potentially involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed miRNA microarray as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation. 5-7 weeks female BALB/c mice, (1) AOM/DSS group: AOM 12.5mg/kg i.p. at day 1, DSS drinking 5d/21dx3circles from day 5; (2) AOM group: AOM 10mg/kg i.p. 1/weekx6 from day 1; (3) DSS group: DSS drinking 5d/21dx3circles from day 5. The distal colon epithelial tissues were collected at day100 when tumor formed in AOM/DSS bearing mice. The miRNA microarray experiments were performed together.

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mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice --- mRNA expression data

Project description:To find out which mRNAs are significantly differential expression and potentially involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation. 5-7 weeks female BALB/c mice, (1) AOM/DSS group: AOM 12.5mg/kg i.p. at day 1, DSS drinking 5d/21dx3circles from day 5; (2) AOM group: AOM 10mg/kg i.p. 1/weekx6 from day 1; (3) DSS group: DSS drinking 5d/21dx3circles from day 5. The distal colon epithelial tissues were collected at day100 when tumor formed in AOM/DSS bearing mice. The whole genome microarray expression profiling experiments were performed together.

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mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice --- miRNA microarray

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and RNF138-/- mice colorectal transcriptomes in DSS, AOM/DSS and organoids samples

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