GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Helicobacter pylori; Oxytricha trifallax; mixed culture metagenome

Type:

Methylation profiling by high throughput sequencing; Other

4 related Platforms

22 Samples

Download data: CSV, TXT

(Submitter supplied) DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. more...

Organism:

Escherichia coli; Oxytricha trifallax

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL30646 GPL21222

10 Samples

Download data: CSV, TXT

(Submitter supplied) DNA N6-adenine methylation (6mA) has recently been reported in diverse eukaryotes, spanning unicellular organisms to metazoans. Yet the functional significance of 6mA remains elusive due to its low abundance, difficulty of manipulation within native DNA, and lack of understanding of eukaryotic 6mA writers. Through biochemical fractionation of nuclear extracts, we identify a putative DNA 6mA methyltransferase in ciliates, termed MTA1. more...

Organism:

Tetrahymena thermophila; Oxytricha trifallax

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26723 GPL18396 GPL23021

77 Samples

Download data: GFF, TXT

(Submitter supplied) Dicer-dependent small non-coding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long non-coding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery. more...

Organism:

Oxytricha trifallax

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platform:

GPL18396

14 Samples

Download data: TXT

(Submitter supplied) As part of sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes, in which hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and amplified dozens of times, to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. more...

Organism:

Oxytricha trifallax

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15459

14 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Oxytricha cells containing a chromosome fusion were backcrossed to wild-type, and the production of novel piRNAs spanning the fusion boundary was demonstrated by PIWI-protein (Otiwi-1) immunoprecipitation - seq

Organism:

Sterkiella histriomuscorum; Oxytricha trifallax

Type:

Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL15927

1 Sample

Download data: FA, FASTA, SAM

(Submitter supplied) To study the biogenesis of long non-coding RNAs transcribed during genome rearrangements in Oxytricha development, genome-wide localization pattern of Rpb1 (RNA Pol-II largest subunit) was studied from Oxytricha cells undergoing conjugation.

Organism:

Oxytricha trifallax

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18396

2 Samples

Download data: TXT

(Submitter supplied) We report the existence of both methylcytosine and hydroxymethylcytosine in the genomic DNA of the ciliate Oxytricha trifallax during its genome rearrangement process. These modifications are dynamically added, de novo, to sequences targeted for elimination and are not present after the rearrangement process (in vegetative cells). We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine.

Organism:

Oxytricha trifallax

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15459

6 Samples

Download data: TXT

(Submitter supplied) In Oxytricha, the somatic genome is responsible for vegetative growth, while the germline contributes DNA to the next sexual generation. Somatic nuclear development eliminates all transposons and other so-called "junk DNA", which constitute ~95% of the germline. We demonstrate that Piwi-interacting small RNAs (piRNAs) from the maternal nucleus can specify genomic regions for retention in this process. more...

Organism:

Oxytricha trifallax

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15459 GPL15927

2 Samples

Download data: FA, TXT

(Submitter supplied) Here we report that soon after mating of Oxytricha trifallax, abundant 27nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of these 27nt RNAs from various times after mating. Using sequence comparisons between macronuclear and micronuclear versions of genes, we found that this 27nt RNA class derives from the parental macronucleus, not the developing macronucleus. more...

Organism:

Oxytricha trifallax

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15459

11 Samples

Download data: TXT