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Items: 20

1.

NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs

(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
Series
Accession:
GSE44386
ID:
200044386
2.

NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [iCLIP]

(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
3.

NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [RNA-seq]

(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
Series
Accession:
GSE44384
ID:
200044384
4.

The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation

(Submitter supplied) Post-transcriptional regulatory mechanisms are crucial for protein synthesis during spermatogenesis and often organized by the chromatoid body. Chromatoid bodies are large cytoplasmic ribonucleoprotein granules, whose precise function and composition remain unclear. Here, we identify NSun2 as a novel component of the chromatoid body, and further show that this RNA methylase is essential for germ cell differentiation in the mouse testis. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6887
24 Samples
Download data: TXT
Series
Accession:
GSE39480
ID:
200039480
5.

Loss of cytosine-5 methylation in tRNA triggers stress responses in a disease model for Intellectual Disability

(Submitter supplied) Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause Intellectual Disability (ID) and symptoms commonly found in patients with Dubowitz syndrome. By analysing gene expression data with the global cytosine-5 RNA methylome in NSun2-deficient mice, we find that loss of cytosine-5 RNA methylation increases the fragmentation of transfer RNAs (tRNA) leading to an accumulation of 5’ halves. Cleavage of tRNAs by Angiogenin is a common cellular stress response to silence translational programmes, and we show that Angiogenin binds tRNAs lacking site-specific NSun2-methylation with higher affinity. Furthermore, cells lacking functional NSun2 up-regulate stress markers, and deletion of NSun2 compromises cellular survival in response stress stimuli including UV-light and oxidative stress. The decreased tolerance of NSun2 null cells towards oxidative stress can be rescued through inhibition of Angiogenin. In conclusion, cytosine-5 RNA methylation is an essential post-transcriptional mechanism during cellular stress responses and NSun2-mediated tRNA methylation protects from Angiogenin-dependent stress-induced RNA cleavage.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
Platform:
GPL9250
21 Samples
Download data: TXT
6.

High resolution transcriptome-wide RNA cytosine methylome of Mouse Embryonic Fibroblasts

(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
Series
Accession:
GSE44359
ID:
200044359
7.

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(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
8.

Conservation of m5C in tRNAs in the kingdom Plantae

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in transfer RNAs of all three sub-cellular transcriptomes across six diverse species that include, the single-celled algae Nannochloropsis oculata, the macro algae Caulerpa taxifolia and multi-cellular higher plants Arabidopsis thaliana, Brassica rapa, Triticum durum and Ginkgo biloba.
Organism:
Brassica rapa; Caulerpa taxifolia; Ginkgo biloba; Arabidopsis thaliana; Triticum turgidum subsp. durum; Nannochloropsis oculata
Type:
Other; Non-coding RNA profiling by high throughput sequencing
6 related Platforms
14 Samples
Download data: XLS, XLSX
9.

Conservation of m5C in rRNA in the kingdom Plantae

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs of all three sub-cellular transcriptomes across six diverse species that included, the single-celled algae Nannochloropsis oculata, the macro algae Caulerpa taxifolia and multi-cellular higher plants Arabidopsis thaliana, Brassica rapa, Triticum durum and Ginkgo biloba. more...
Organism:
Ginkgo biloba; Triticum turgidum subsp. durum; Caulerpa taxifolia; Arabidopsis thaliana; Brassica rapa; Nannochloropsis oculata
Type:
Other; Non-coding RNA profiling by high throughput sequencing
6 related Platforms
13 Samples
Download data: XLSX
10.

tRNA 5-methylcytosine in Arabidopsis thaliana

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in transfer RNAs of all three sub-cellular transcriptomes of Arabidopsis thaliana. 5-methylcytosine sites in tRNAs were also determined in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5 and NOP2A.
Organism:
Arabidopsis thaliana
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17970
11 Samples
Download data: XLS, XLSX
11.

rRNA 5-methylcytosine in Arabidopsis thaliana

(Submitter supplied) Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in ribosomal RNAs of all three sub-cellular transcriptomes in Arabidopsis thaliana. m5C sites in rRNAs were also anlyzed in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5, NOP2A, NOP2B and NOP2C.
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing; Other
Platform:
GPL17970
25 Samples
Download data: XLS, XLSX
12.

The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs

(Submitter supplied) Vault particles are conserved organelles that have been implicated in multidrug resistance and intracellular transport. They are formed by three different proteins and the non-coding vault RNAs (vRNAs). Here we show that human vRNAs produce several small RNAs (svRNAs) by mechanisms different from the canonical microRNA (miRNA) pathway. At least one of these svRNAs, we named svRNAb, associates with Argonaute proteins to guide sequence-specific cleavage and regulate gene expression in a manner similar to miRNAs. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9052
1 Sample
Download data
Series
Accession:
GSE16060
ID:
200016060
13.

RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites

(Submitter supplied) We developed a general method based on RNA Antisense Purification (RAP) to identify the intermolecular RNA-RNA interactions of a target RNA (RAP-RNA). RAP-RNA identifies endogenous RNA-RNA complexes through in vivo crosslinking, RNA capture with antisense oligonucleotides, and high-throughput RNA sequencing. This approach provides a systematic view of other RNAs that interact with a target RNA, and furthermore can distinguish between direct and indirect RNA-RNA interactions through the use of crosslinking reagents with different reactivities with proteins and nucleic acids. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL17021
46 Samples
Download data: BIGWIG, FA, TDF
14.

RNA-seq HL60 cells

(Submitter supplied) Identification of the all RNA species coding and non-coding in total RNA
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
2 Samples
Download data: GTF
Series
Accession:
GSE41279
ID:
200041279
15.

Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL11154 GPL6244 GPL10999
8 Samples
Download data: BSP, CEL, GTF, WIG
Series
Accession:
GSE32260
ID:
200032260
16.

RRBS (Reduced Representation Bisulfite Sequencing) of HL60

(Submitter supplied) We exploited the methylation genome-scale screening RRBS to correlate the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci. Out of 15275 non ambiguous gene loci identified by DNMT1 RIP-Seq, 9436 loci were covered by RRBS. These 9436 loci were clustered according to the fold of specific DNMT1 library peaks enrichment (defined as the ratio of the sum of the area under the curve of specific DNMT1 library peaks covering the gene loci). more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL10999
2 Samples
Download data: BSP
Series
Accession:
GSE32168
ID:
200032168
17.

RIPSEQ DNMT1 HL60

(Submitter supplied) Identification of the all RNA species associated with DNMT1. Using a comparative genome-scale approach we identified and correlated the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci and expression levels of the respective genes. This comparative approach delineated the first -DNMT1 centered- 'epitranscriptome' map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL10999
2 Samples
Download data: WIG
Series
Accession:
GSE32162
ID:
200032162
18.

Expression data from WT HL60 cells

(Submitter supplied) We used the microarray analysis to detail the gene expression profile from the leukemic cell line HL-60
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
2 Samples
Download data: CEL
Series
Accession:
GSE32153
ID:
200032153
19.

Dissecting non-coding and pathogen RNA-protein interactomes

(Submitter supplied) RNA-protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and non-human RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and non-human transcriptomes. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL16791
2 Samples
Download data: BW
Series
Accession:
GSE59840
ID:
200059840
20.

Global identification and characterization of intermediate-size non-coding RNAs in Oryza sativa

(Submitter supplied) In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. more...
Organism:
Oryza sativa
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL15856
2 Samples
Download data: BED
Series
Accession:
GSE39695
ID:
200039695
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