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Next Generation Sequencing Facilitates Quantitative Analysis of Original and RCHO-resistant NU-DUL-1 cell Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Original and RCHO-resistant NU-DUL-1 cell Transcriptomes

PROVIDER: PRJNA449711 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6984690.fastq.gz	Fastqsanger.gz
	SRR6984691.fastq.gz	Fastqsanger.gz
	SRR6984692.fastq.gz	Fastqsanger.gz
	SRR6984693.fastq.gz	Fastqsanger.gz
	SRR6984694.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Original and RCHO-resistant NU-DUL-1 cell Transcriptomes

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Project description:Purpose: we aimed at identify and compare the transcriptional changes of ALDH- and ALDH+ DU145 xenografts upon radiotherapy treatment. Method: Xenografts were generated by injection of ALDH- and ALDH+ DU145 cells in male NMRI-Foxn1 nu/nu immune-deficient mice and subjected to fractionated irradiation to a final dose of 50 Gy. Tumors were excised and processed for total RNA extraction and RNAseq analysis.

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Project description:The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of original E. coli K-12 MG1655 and fluoxetine induced E. coli mutants in response to 100 mg/L fluoxetine for 8 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

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Lactobacillus phage Lc-Nu

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Genome-wide analysis of gene expression profile of Xenograft Tumors (HT29 cells) grown in Nu/Nu Athymic Female Mice infected with Control (Ad-VP16) or LXRa (VP16hLXRa) Adenovirus

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