GEO DataSets

(Submitter supplied) We report development of a mechanism-based technique, Aza-IP, that utilizes the stable covalent linkage formed in vivo between an RNA methyltransferase (m5C-RMT) and 5-azacytidine (5-aza-C) incorporated within the target RNA to enable specific target enrichment, coupled with high-throughput sequencing to provide target identification. We apply Aza-IP to two enzyme types, DNMT2 and NSUN2, the latter with important roles in fertility, intellectual ability, stem cells and cancer. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

7 Samples

Download data: XLS

(Submitter supplied) We report high resolution transcriptome-wide RNA cytosine methylome of Mouse Embryonic Fibroblasts (MEFs) revealed by an optimized new RNA bisulfite sequencing approach. Comparison of RNA methylation profile from wild-type and Dnmt2 -/- MEFs shows that only C38 in three tRNAs (tRNA-Asp, Gly and Val) is the target of Dnmt2 in MEFs at normal conditions.

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

8 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9115

14 Samples

Download data: TXT

(Submitter supplied) Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we adapted the individual-nucleotide resolution UV cross-linking and immunoprecipitation method (iCLIP) to identify NSun2-mediated methylation in RNA transcriptome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9115

6 Samples

Download data: TXT

(Submitter supplied) Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we adapted the individual-nucleotide resolution UV cross-linking and immunoprecipitation method (iCLIP) to identify NSun2-mediated methylation in RNA transcriptome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

8 Samples

Download data: TXT

(Submitter supplied) Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNAs, and is formed via catalytic conversion of uridines. In yeast, m5U is known to be present at position 54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

14 Samples

Download data: BED

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

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: TXT

(Submitter supplied) (Cytosine-5) RNA methylation plays an important role in several biologically and pathologically relevant processes. However, owing to methodological limitations, the transcriptome-wide distribution of this mark has remained largely unknown. We have previously established RNA bisulfite sequencing as a method for the analysis of RNA (cytosine-5) methylation patterns at single-base resolution. Furthermore, next-generation sequencing has provided opportunities to establish transcriptome-wide maps of this modification. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: TXT

(Submitter supplied) (Cytosine-5) RNA methylation plays an important role in several biologically and pathologically relevant processes. However, owing to methodological limitations, the transcriptome-wide distribution of this mark has remained largely unknown. We have previously established RNA bisulfite sequencing as a method for the analysis of RNA (cytosine-5) methylation patterns at single-base resolution. Furthermore, next-generation sequencing has provided opportunities to establish transcriptome-wide maps of this modification. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

16 Samples

Download data: TXT

(Submitter supplied) Dnmt2 and NSun2 are (cytosine-5) RNA methyltransferases. Using CRISPR/Cas9 we created null mutations in Dnmt2 and NSun2 genes in Drosophila melanogaster. We also ectopically expressed a wild type and catalytically inactive Dnmt2 form in the Dnmt2 mutant background. RNA bisulfite sequencing was used to follow RNA methylation at partical tRNA substrates.

Organism:

Drosophila melanogaster

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16479

16 Samples

Download data: TXT

(Submitter supplied) It has been claimed previously that loss of (cytosine-5) DNA methylation in Dnmt2 mutant embryos affected the establishment of silent chromatin at Invader4 LTRs (Phalke et al., 2009). The inability of Dnmt2 mutants to control TE expression after heat shock (GSE40432) raised the possibility that DNA methylation could be required for control of Invader 4 during the heat shock response. We used DNA bisulfite sequencing at Inv4 LTRs that were previously suggested to be methylated (Phalke et al., 2009).

Organism:

Drosophila melanogaster

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23840

8 Samples

Download data: TXT

(Submitter supplied) Dnmt2 genes are highly conserved tRNA methyltransferases with biological roles in cellular stress responses. Dnmt2 has recently been implicated in transposon silencing in Drosophila but the exact molecular mechanisms are unclear. Adult Dnmt2 mutants were heat shocked and RNA sequencing was performed on visible high-molecular weight RNAs to determine the identity of up-regulated transposons. Dnmt2 mutants accumulated almost all families of transposons after heat shock, indicating a general mis-regulation of transposon silencing in Dnmt2 mutants during the stress response.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

1 Sample

Download data: TXT