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Items: 1 to 20 of 676

1.

Recovery of Tetrahymena thermophila from degranulation

(Submitter supplied) The object was to identify genes that are upregulated during the recovery of cells from stimulation of granule exocytosis, when new granules are being synthesized. The granules are also known as mucocysts. To distinguish between genes upregulated due to demands of granule synthesis, vs genes upregulated in response to the exocytic stimulus per se, we exploited a mutant cell line, MN173, that does not release its granules on stimulation.
Organism:
Tetrahymena thermophila
Type:
Expression profiling by array
Platform:
GPL6759
12 Samples
Download data: TXT
Series
Accession:
GSE276404
ID:
200276404
2.

EMA2 is required for target-directed scnRNA degradation.

(Submitter supplied) Piwi-associated small RNAs of the ciliated protozoan Tetrahymena uses such mechanism to induce heterochromatin formation followed by programmed DNA elimination. In this process, target-directed small RNA degradation (TDSD) of small RNAs complementary to the somatic genome enables small RNAs to specifically target the germline-limited sequences for DNA elimination. The data here indicate that the SUMO E3 ligase Ema2 is required for the accumulation of long non-coding RNAs (lncRNAs) from the somatic genome and thus for TDSD.
Organism:
Tetrahymena thermophila
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL15706
4 Samples
Download data: FASTA, TXT
Series
Accession:
GSE243435
ID:
200243435
3.

Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Tetrahymena thermophila
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL32089
8 Samples
Download data: BW
Series
Accession:
GSE210903
ID:
200210903
4.

Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena [RNA-seq]

(Submitter supplied) Through epigenetic modifications and selective incorporation of histone variants into chromatin, eukaryotic cells can adjust their transcriptional profile in response to molecular needs. We used the nuclear dimorphic ciliate protozoan, Tetrahymena thermophila, as a model system to investigate the dynamics of H3 variant function. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. more...
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32089
4 Samples
Download data: TXT
Series
Accession:
GSE210902
ID:
200210902
5.

Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena [ChIP-seq]

(Submitter supplied) Through epigenetic modifications and selective incorporation of histone variants into chromatin, eukaryotic cells can adjust their transcriptional profile in response to molecular needs. We used the nuclear dimorphic ciliate protozoan, Tetrahymena thermophila, as a model system to investigate the dynamics of H3 variant function. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. more...
Organism:
Tetrahymena thermophila
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL32089
4 Samples
Download data: BW, TXT
Series
Accession:
GSE210901
ID:
200210901
6.

Investigation of small RNA biogenesis and turnover in the absence of the PRC2 associated protein Ded2p

(Submitter supplied) Heterochromatic histone H3 methylation at lysine 9 (H3K9me2/3) and lysine 27 (H3K27me3) is generally catalyzed by SUV39 and EZH family methyltransferases, respectively, and has distinct functions in most eukaryotes. In contrast, the ciliated protozoan Tetrahymena lacks the SUV39 enzyme, and the EZH enzyme Ezl1p is responsible for the deposition of both H3K9me3 and H3K27me3 during Piwi-directed DNA elimination. more...
Organism:
Tetrahymena thermophila
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL15706
6 Samples
Download data: TXT
Series
Accession:
GSE190308
ID:
200190308
7.

Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles

(Submitter supplied) As a prototypic ciliated protozoan, Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During the vegetative phase of the life cycle, the S phases of the diploid germline micronucleus and polyploid somatic macronucleus are temporally offset. Here we report the first RNA-Seq analysis across the cell cycle of a binucleated ciliated protozoan. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23968
18 Samples
Download data: CSV
Series
Accession:
GSE209619
ID:
200209619
8.

An altered basis of tRNA processing is linked to a distinct La protein in T. thermophila

(Submitter supplied) La proteins bind the UUU-3’OH sequence found at the 3’-end of nascent RNA polymerase III transcripts, including pre-tRNAs, using a tandem arrangement of a winged-helix fold La motif (LaM) and an adjacent RNA recognition motif (RRM). La binding in diverse species results in protection of the 3’-end from exonucleases, stabilization of the pre-tRNA species and promotion of pre-tRNA folding until the UUU-3’OH containing trailer is endonucleolytically cleaved. more...
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32089
9 Samples
Download data: XLSX
Series
Accession:
GSE199642
ID:
200199642
9.

mRNA sequencing of WT, ∆MTA and ∆MTB cells in Starvation, costimulation and early Conjugation of Tetrahymena thermophila.

(Submitter supplied) The goals of this study is to investigate the function of MTA and MTB of Tetrahymena thermophila.
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21412
7 Samples
Download data: TXT
Series
Accession:
GSE143928
ID:
200143928
10.

Epigenetic effects of silver nanoparticles and ionic silver in Tetrahymena thermophila

(Submitter supplied) The widespread use of silver nanoparticles (Ag NPs) has raised substantial health risks to environmental and human beings. Although various negative effects had been reported, little is known about the epigenetic toxicity induced by Ag+ and Ag NPs. This study characterized physiological and lncRNA profiles to explore the toxic effects and epigenetic mechanisms in Tetrahymena thermophila on exposure to Ag+ and three types of Ag NPs. more...
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL26097
15 Samples
Download data: XLS
Series
Accession:
GSE157616
ID:
200157616
11.

Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of RBBP4/7 ortholog in Tetrahymena thermophila

(Submitter supplied) Retinoblastoma-binding proteins 4 and 7 (RBBP4 and 7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Genome-wide analyses indicated that RebL1 and Tetrahymena Lin54 (Anqa1) bind predominantly within genic regions. more...
Organism:
Tetrahymena thermophila
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL23968
8 Samples
Download data: TXT
Series
Accession:
GSE156091
ID:
200156091
12.

Distinct 3D Genome Organization in the Two Nuclei of Tetrahymena thermophila

(Submitter supplied) Somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila are different in chromosome numbers, sizes, functions and cohesin complex locations. Loss of cohesin complex resulted in genome-wide disappearance of topologically associating domains (TADs) and chromatin loops in mammalian cells. However, the higher-level chromatin organization in Tetrahymena thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. more...
Organism:
Tetrahymena thermophila
Type:
Other
Platform:
GPL26097
18 Samples
Download data: HIC, TXT
Series
Accession:
GSE125628
ID:
200125628
13.

Determination of isoform-specific RNA structure with nanopore long reads

(Submitter supplied) Current methods for determening RNA structure with short-read sequencing cannot capture most differences between distinct transcript isoforms. Here, we present RNA structure analysis using nanopore sequencing (PORE-cupine),which combines structure probing using chemical modifications with direct long-read RNA sequencing and machine learning to detect secondary structures in cellular RNAs. PORE-cupine also captures global structural features, such as RNA binding protein (RBP) binding sites and reactivity differences at single nucleotide variants (SNVs). more...
Organism:
Bacillus subtilis; Saccharomyces cerevisiae; Homo sapiens; Dengue virus; Oceanobacillus iheyensis; Tetrahymena thermophila
Type:
Other
5 related Platforms
21 Samples
Download data: CSV, TAR, TXT, XLSX
Series
Accession:
GSE133361
ID:
200133361
14.

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

(Submitter supplied) The goals of this study is to investigate the function of CDK19 and CYC9 of Tetrahymena thermophila.
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21412
6 Samples
Download data: TXT
Series
Accession:
GSE132677
ID:
200132677
15.

Tetrahymena thermophila macronucleus chromosomes originate from chromatin breakage sequence defined TAD-like structures in micronucleus chromosomes

(Submitter supplied) The somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila differ in chromosome numbers, sizes, functions, transcriptional activities, and cohesin complex location. However, the higher-order chromatin organization in T. thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. Here, we examined the higher-order chromatin organization in the two distinct nuclei of T. more...
Organism:
Tetrahymena thermophila
Type:
Other
Platform:
GPL26097
18 Samples
Download data: HIC
Series
Accession:
GSE140429
ID:
200140429
16.

Gene expression of Tetrahymena thermophila SB210 under the arsenic exposure

(Submitter supplied) To identified the differential expressed genes between the arsenic exposure cells and wild type cells As is a well- known carcinogen, it receives special attention. Due to its ubiquitous distribution in the environment, a unicellular model system related to the environment will be useful in toxicological research of arsenic. The eukaryotic protist Tetrahymena thermophila is a well-established model in classical toxicology and now a potential model at genomic level. more...
Organism:
Tetrahymena thermophila SB210; Tetrahymena thermophila
Type:
Expression profiling by array
Platform:
GPL6759
8 Samples
Download data: PAIR
Series
Accession:
GSE53836
ID:
200053836
17.

Transcriptional response of Tetrahymena thermophila to exogenous cholesterol

(Submitter supplied) The model ciliate Tetrahymena thermophila satisfies its growth using triterpenoid alcohols, mainly tetrahymanol, as a surrogate of sterols. When sterols are present in the environment, T. thermophila efficiently incorporates and modifies them. T. thermophila can modify exogenous sterols by desaturation at positions C5(6), C7(8) and C22(23), and also by de-ethylation of C24. Three out of four of the enzymes involved in the sterol modification pathway were previously described by our group. more...
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15706
6 Samples
Download data: TXT
Series
Accession:
GSE130336
ID:
200130336
18.

Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

(Submitter supplied) In order to resolve controversies concerning SMYD's substrates and functions, we studied SMYD1 (TTHERM_00578660), the only homologue in the unicellular eukaryote Tetrahymena thermophila. We epitope-tagged SMYD1, and analyzed its localization and interactome. We also characterized ΔSMYD1 cells, focusing on the replication and transcription phenotype. Our results show that: 1) SMYD1 is present in both cytoplasm and transcriptionally active macronucleus and shuttles between cytoplasm and macronucleus, which is consistent with its association with both histone and non-histone substrates; 2) SMYD1 is involved in DNA replication and regulates transcription of metabolism-related genes; 3) HSP90 is an potential substrate for SMYD1 and it may regulate target selection of HSP90, leading to pleiotropic effects in both the cytoplasm and the nucleus.
Organism:
Tetrahymena thermophila
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23968
2 Samples
Download data: TXT
Series
Accession:
GSE138246
ID:
200138246
19.

RACS: Rapid Analysis of ChIP-Seq data for contig based genomes

(Submitter supplied) The biological samples are from untagged Tetrahymena thermophila to be used as a control for unspecific binding. Whole cells extracts were crosslinked and immunoprecipitated using M2 affinity gel (Sigma). The obtained DNA was sequenced by HiSeq2500 (Illumina). The processed fastq files were analyzed by RACS that segregates the found read accumulations between genic and intergenic regions being highly efficient for rapid downstream analyses.
Organism:
Tetrahymena thermophila
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL23968
8 Samples
Download data: CSV
Series
Accession:
GSE125576
ID:
200125576
20.

ChIP-Seq Analysis of Med31-FZZ

(Submitter supplied) The biological samples are from Med31-FZZ tagged Tetrahymena thermophila. Whole cells extracts were crosslinked and immunoprecipitated using M2 affinity gel (Sigma). The obtained DNA was sequenced by HiSeq2500 (Illumina). The processed fastq files were analyzed by RACS that segregates the found read accumulations between genic and intergenic regions being highly efficient for rapid downstream analyses.
Organism:
Tetrahymena thermophila
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL23968
4 Samples
Download data: CSV
Series
Accession:
GSE126344
ID:
200126344
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