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MRNA sequencing of WT, ∆CDK19 and ∆CYC9 cells in starvation and costimulation (S, co) of Tetrahymena thermophila

ABSTRACT: mRNA sequencing of WT, ∆CDK19 and ∆CYC9 cells in starvation and costimulation (S, co) of Tetrahymena thermophila

PROVIDER: PRJNA548743 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9291614_1.fastq.gz	Fastqsanger.gz
	SRR9291614_2.fastq.gz	Fastqsanger.gz
	SRR9291615_1.fastq.gz	Fastqsanger.gz
	SRR9291615_2.fastq.gz	Fastqsanger.gz
	SRR9291616_1.fastq.gz	Fastqsanger.gz

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mRNA sequencing of WT, ∆CDK19 and ∆CYC9 cells in starvation and costimulation (S, co) of Tetrahymena thermophila

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Genome-Wide Microarray Analysis of Gene Expression During Starvation in Tetrahymena thermophila

Project description:Two genome-wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila were used to study gene expression in starved cells (starvation 0 hour and starvation 24 hour). Combining these two microarrays with 50 microarrays described in Miao et al. (2009) and 15 other microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human. For starvation, CU428 cells were starved at 2x10^5 cells/ml in 10 mM Tris (pH 7.5) for 0 and 24 hours (referred to as S-0 and S-24, respectively).

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Project description:Four genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in starved cells (Starvation 0 hour and Starvation 9 hour, each two replicates). Combined these four microarrays with 50 microarrays described in Miao et al (2009, PMID: 19204800; GSE11300) and other 13 microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human. For starvation, CU427 cells were starved at 2x10^5 cells/ml in 10 mM Tris (pH 7.5) for 0 and 9 hours (referred to as S-0 and S-9, respectively).

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