GEO DataSets

(Submitter supplied) 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. more...

Organism:

Tetrahymena thermophila

Type:

Expression profiling by array

Platform:

GPL6759

50 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Tetrahymena thermophila

Type:

Expression profiling by array

Platform:

GPL6759

11 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Tetrahymena thermophila

Type:

Expression profiling by array

Platform:

GPL6759

4 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Tetrahymena thermophila

Type:

Expression profiling by array

Platform:

GPL6759

2 Samples

Download data: PAIR

(Submitter supplied) 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. more...

Organism:

Tetrahymena thermophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9367

6 Samples

Download data: TXT

(Submitter supplied) The goals of this study is to investigate the function of E2fl-1 of Tetrahymena thermophila.

Organism:

Tetrahymena thermophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21412

12 Samples

Download data: TXT

(Submitter supplied) We hypothesize that Ibd1 coordinates the recruitment of several chromatin remodeling complexes to promote transcription of highly expressed genes in T.thermophila. We developed a ChIP-seq protocol including a heuristic method (in preparation paper, Ponce & Saettone, et al., 2017) to call peaks present in genic and intergenic regions specifically. We used the obtained data from the 2 NGS biological replicas, each of which had an INPUT and an Immunoprecipitated (IP) sample.

Organism:

Tetrahymena thermophila

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23968

4 Samples

Download data: XLS, XLSX

(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

(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

(Submitter supplied) The goals of this study is to investigate the function of Cdk3 of Tetrahymena thermophila.

Organism:

Tetrahymena thermophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21412

6 Samples

Download data: TXT

(Submitter supplied) 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 2.5–3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. more...

Organism:

Tetrahymena thermophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21412

8 Samples

Download data: XLSX

(Submitter supplied) The goals of this study are to investigate the function of Dpl2 of Tetrahymena thermophila.

Organism:

Tetrahymena thermophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21412

10 Samples

Download data: TXT

(Submitter supplied) The goals of this study is to investigate the function of Cyc17 of Tetrahymena thermophila.

Organism:

Tetrahymena thermophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21412

8 Samples

Download data: TXT

(Submitter supplied) PAZ/PIWI-domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi-family proteins (Twis) preferentially expressed in growing cells differ in their genetic essentiality and subcellular localization. Affinity purification of all eight distinct Twi proteins revealed unique properties of their bound sRNAs. more...

Organism:

Tetrahymena thermophila

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9367

11 Samples

Download data: CSV

(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

(Submitter supplied) A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study. Custom cDNA microarrays were constructed for P. pelagicus. The printed arrays contained 5000 transcripts derived from both the whole organism, and from individual organs such as the brain, eyestalk, mandibular organ and Y-organ from all moult cycle stages. more...

Organism:

Portunus pelagicus

Type:

Expression profiling by array

Platform:

GPL4797

30 Samples

Download data

(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

(Submitter supplied) This study describes the application of the LongSAGE methodology to study the gene expression profile in Leishmania infantum chagasi. A tag library was created using the LongSAGE method and consisted of 14,208 tags of 17 bases. Of these, 8,427 (59.3%) were distinct. BLAST research of the 1,645 most abundant tags showed that 12.8% of them identified the coding sequences of genes, while 82% (1,349/1,645) identified one or more genomic sequences that did not correspond with open reading frames. more...

Organism:

Leishmania chagasi

Type:

Expression profiling by SAGE

Platform:

GPL11414

1 Sample

Download data

(Submitter supplied) modENCODE_submission_3173 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array

Platform:

GPL5634

3 Samples

Download data: BEDGRAPH, CEL, GFF3

(Submitter supplied) modENCODE_submission_3172 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array

Platform:

GPL5634

3 Samples

Download data: BEDGRAPH, CEL, GFF3