MRNA sequencing of WT, ∆MTA and ∆MTB cells in Starvation, costimulation and early Conjugation of Tetrahymena thermophila.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA602178 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10915512_1.fastq.gz | Fastqsanger.gz | |||
| SRR10915512_2.fastq.gz | Fastqsanger.gz | |||
| SRR10915513_1.fastq.gz | Fastqsanger.gz | |||
| SRR10915513_2.fastq.gz | Fastqsanger.gz | |||
| SRR10915514_1.fastq.gz | Fastqsanger.gz |
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Project description:The goals of this study is to investigate the function of MTA and MTB of Tetrahymena thermophila.
2022-02-02 | GSE143928 | GEO
Project description:Eleven genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in conjugation cells (C-0, C-15m, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16, C-18). Combined these eleven microarrays with 50 microarrays described in Miao et al (2009) and other 6 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 conjugation, B2086 and CU428 cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 200,000 cells/ml, mixed, and samples were collected at 15 min, 2, 4, 6, 8, 10, 12, 14, 16, 18 hours after the mixture （referred to as C-0, C-15m, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16 and C-18).
2011-06-13 | E-GEOD-26650 | biostudies-arrayexpress
Project description:We present a comprehensive transcriptome of ciliate T. thermophila using the Illumina RNA-seq platform. The data was generated from the six mRNA samples of growth, starvation and conjugation of Tetrahymena. Despite an AT rich genome, there are about 124.6 million reads mapped to T. thermophila genome. Using these mapped reads, we have significantly improved the previous genome annotation and investigated the gene expression. Besides, our result also provided a comprehensive understanding of the alternative splicing in T. thermophila, and suggested the existence of the regulated unproductive splicing and translation (RUST) in the single-celled eukaryote. RNA-seq for six samples of Tetrahymena growth, starvation and conjugation.
2012-03-15 | E-GEOD-27971 | biostudies-arrayexpress
Project description:Eleven genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in conjugation cells (C-0, C-15m, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16, C-18). Combined these eleven microarrays with 50 microarrays described in Miao et al (2009) and other 6 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.
2011-06-13 | GSE26650 | GEO
Project description:A genome wide microarray platform containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila is described, validated and used to study gene expression in growing, starved and conjugating cells. Of the ~27,400 predicted open reading frames in Tetrahymena, transcripts homologous to 5876 are not detectable in one or more of these life cycle stages, indicating that this organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels 5X background and 95 genes are expressed at 250X background in all stages. Transcripts homologous to 94 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, and 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1073 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the previously described developmental stages of meiosis, nuclear differentiation and DNA elimination. Genes encoding proteins known to be complexed show similar expression patterns, indicating that co-ordinate expression with putative genes of known function should identify new genes with related functions. Keywords: growth (three cell densities); Starvation (seven time points); Conjugation (ten time points)
2008-10-01 | GSE11300 | GEO
Project description:A genome wide microarray platform containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila is described, validated and used to study gene expression in growing, starved and conjugating cells. Of the ~27,400 predicted open reading frames in Tetrahymena, transcripts homologous to 5876 are not detectable in one or more of these life cycle stages, indicating that this organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels 5X background and 95 genes are expressed at 250X background in all stages. Transcripts homologous to 94 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, and 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1073 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the previously described developmental stages of meiosis, nuclear differentiation and DNA elimination. Genes encoding proteins known to be complexed show similar expression patterns, indicating that co-ordinate expression with putative genes of known function should identify new genes with related functions. Keywords: growth (three cell densities); Starvation (seven time points); Conjugation (ten time points) For growth, CU428 cells at low, medium and high cell densities (~100Kcells/ml, ~350Kcells/ml and ~1000Kcells/ml; referred to as L-l, L-m and L-h) were collected. For starvation, CU428 cells were starved at 2x105 cells/ml in 10 mM Tris (pH 7.5) for 3, 6, 9, 12, 15 and 24 hours ï¼referred to as S-0, S-3, S-6, S-9, S-12, S-15 and S-24. For conjugation, B2086 and CU428 cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 2x105 cells/ml, mixed, and samples were collected at 2, 4, 6, 8, 10, 12, 14, 16, 18 hours after the mixture ï¼referred to as C-0, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16 and C-18). For each growing and starved Tetrahymena sample, hybridizations were performed on three independent microarrays (e.g. L1, L2 and L3; S1, S2 and S3). For analysis of conjugation, hybridizations were performed on two independent microarrays (e.g. C1 and C2). Each individual microarray represents a separate experiment; total RNA was isolated from independent cell cultures then independently labeled and hybridized.
2010-06-25 | E-GEOD-11300 | biostudies-arrayexpress
Project description:Genome-Wide gene expression of Tetrahymena thermophila conjugation
| PRJNA136385 | ENA
Project description:We present a comprehensive transcriptome of ciliate T. thermophila using the Illumina RNA-seq platform. The data was generated from the six mRNA samples of growth, starvation and conjugation of Tetrahymena. Despite an AT rich genome, there are about 124.6 million reads mapped to T. thermophila genome. Using these mapped reads, we have significantly improved the previous genome annotation and investigated the gene expression. Besides, our result also provided a comprehensive understanding of the alternative splicing in T. thermophila, and suggested the existence of the regulated unproductive splicing and translation (RUST) in the single-celled eukaryote.
2012-03-15 | GSE27971 | GEO
Project description:The goals of this study is to investigate the function of CDK19 and CYC9 of Tetrahymena thermophila.
2020-03-18 | GSE132677 | GEO
Project description:Meiotic recombination is carried out through a specialized pathway for the formation and repair of DNA double-strand breaks (DSBs) made by the Spo11 protein. The present study shed light on the functional role of Cyclin, CYC2, in Tetrahymena thermophila which has transcriptionally high expression level during meiosis process. Knocking out the CYC2 gene results in arrest of meiotic conjugation process at 2.5â??3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. To investigate the underlying mechanism of this phenomenon, a complete transcriptome profile was performed between wild-type strain and CYC2 knock-out strain. Functional analysis of RNA-Seq results identifies related differentially expressed genes (DEGs) including SPO11 and these DEGs are enriched in DNA repair/mismatch repair (MMR) terms in homologous recombination (HR), which indicates that CYC2 could play a crucial role in meiosis by regulating SPO11 and participating in HR. We performed mRNA profiling on both wild-type strains and CYC2-knocking out strains at four different stages during meiosis prohase of Tetrahymena thermophila.
2016-04-06 | E-GEOD-79286 | biostudies-arrayexpress