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ABSTRACT: mRNA Sequence of mouse tumor

PROVIDER: PRJNA1121486 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR29327188_1.fastq.gz	Fastqsanger.gz
	SRR29327188_2.fastq.gz	Fastqsanger.gz
	SRR29327189_1.fastq.gz	Fastqsanger.gz
	SRR29327189_2.fastq.gz	Fastqsanger.gz
	SRR29327190_1.fastq.gz	Fastqsanger.gz

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Project description:We used a novel probe-level microarray analysis, revealing connections between mRNA processing and lymphoid neoplasia, in a mouse leukemia model. Characteristic differences in mRNA processing, primarily in the 3’-untranslated region, distinguished histologically similar tumor subtypes with different survival characteristics. Gene sets with specific processing in each tumor subtype defined signatures useful for tumor subclassification, as demonstrated by internal cross-validation with up to 80% discrimination accuracy. A combination of mRNA expression and sequence analysis suggested that differences in isoform abundance likely arose from both alternative polyadenylation and differential degradation. Experiment Overall Design: 5 types of samples were analyzed with multiple biological replicates. Progenitor B-cells, mature B-cells were the control. LPC, APC, APN were the tumor cells. LPC (Lig4/P53 deficient cells developed pro-B lymphoma with c-myc amplification), APC (Artemis/P53 deficient cells developed pro-B lymphoma with c-myc amplification), APN (Artemis/P53 deficient cells developed pro-B lymphoma with N-myc amplification)

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Project description:Purpose: We tested global gene transcriptome changes by RNA-sequencing analysis in the offspring breast tumors of SV40 transgenic mice to further identify key epigenetic-controlled genes in regulation of the prenatal/maternal BSp diet-mediated early breast cancer prevention. Method: Mouse offspring mammary tumor mRNA from control and maternal BSp treatment were generated by deep sequencing, in duplicate or triplicate, using Illumina NextSeq500 platform (GPL19057). The sequence reads that passed quality filters were analyzed. We utilized the R/Bioconductor package DESeq to evaluate differential gene expression for sequence count data by the use of negative binomial distributio. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our data showed differential transcriptome distribution in the breast tumors of mouse offspring between the control and prenatal/maternal BSp treatment groups.

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