GEO DataSets

(Submitter supplied) RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

82 Samples

Download data: TXT

(Submitter supplied) Emerging evidence suggests that changes in ribosomal RNA 2’O-ribose methylation (rRNA 2’OMe) in the human ribosome play a key role in regulating translation thereby contributing in setting particular phenotypes such as hallmarks of cancer cells. Here, by analysing the rRNA 2’OMe in a large series of 195 human primary breast tumours using the RiboMETH-seq approach we have identified the positions within the rRNA molecules which can tolerate the absence of 2’OMe in humans. more...

Organism:

Homo sapiens

Type:

Other; Methylation profiling by high throughput sequencing

Platform:

GPL11154

200 Samples

Download data: TSV

(Submitter supplied) Using a technique based on the ability of CMC to specifically label pseudouridines and to stop reverse transcriptase, we provide a transcriptome-wide map of pseudouridylation in S. cerevisiae under log phase and heat shock conditions

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL9377

16 Samples

Download data: TXT

(Submitter supplied) We report the development of Pseudo-Seq, a sequencing based technique for identification of pseuoduridine (Ψ) modifications within RNA. We performed Pseudo-Seq on S. cerevisiae and HeLa cells and find the first evidence for pseusouridylation of endogenous mRNAs.

Organism:

Homo sapiens; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL13821

109 Samples

Download data: TXT, WIG

(Submitter supplied) We performed ribosome profiling on wild-type and METTL5 KO mice to investigate translation changes due to loss of METTL5.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

12 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL24247

28 Samples

Download data

(Submitter supplied) We report the application of MeRIP-seq to map m6A peaks in wild type and METTL5 KO HeLa cells to investigate targets of the m6A methyltransferase METTL5.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) We performed ribosome profiling on wild-type and METTL5 KO HepG2 cells to investigate translation changes due to loss of METTL5.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) We report the application of next-generation sequencing to analyze the transcriptomes of brains and livers of WT and METTL5 KO mice to understand the role(s) of METTL5 in these organs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) Pseudouridine is the most abundant modification occurring on RNA, yet with the exception of a few well-studied RNA molecules little is known about the modified positions and their function(s). Here, we develop Ψ-seq, a method for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with synthetic spike-ins and de novo identification of the vast majority of previously reported pseudouridylated positions. more...

Organism:

Candida albicans; Homo sapiens; Saccharomyces cerevisiae; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

86 Samples

Download data: TXT

(Submitter supplied) Pseudouridine (Ψ) is the most abundant RNA modification, yet little is known about its content, dynamics and function in mRNA and ncRNA. Here, we perform quantitative MS analysis and develop CAP-seq for transcriptome-wide Ψ profiling. The unexpected high Ψ content (Ψ/U ratio: ~ 0.2% to 0.6%) indicates that pseudouridylation in mammalian mRNA is much more prevalent and comprehensive than previously believed. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL11154 GPL17021 GPL16791

34 Samples

Download data: TXT

(Submitter supplied) Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, non-coding RNA and has recently been discovered on mRNA. Transcriptome-wide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organism Dro­­­­sophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL22106

22 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17303 GPL30173 GPL18573

36 Samples

Download data: XLSX

(Submitter supplied) FUS is a nucleocytoplasmic protein involved in many processes such as RNA transport, translation, and metabolism as well as genomic maintenance. FUS mutations are found in several neurodegenerative diseases. We find that FUS knockout (KO) and FUS mutation affects the expression of many C/D box snoRNAs, H/ACA box snoRNAs and scaRNAs. snoRNAs notably serve as adaptors for the 2'-O-methylation (2'-O-me) and pseudouridylation of ribosomal RNA (rRNA).

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) FUS is a nucleocytoplasmic protein involved in many processes such as RNA transport, translation, and metabolism as well as genomic maintenance. FUS mutations are found in several neurodegenerative diseases. We find that FUS knockout (KO) affects the expression of many C/D box snoRNAs, H/ACA box snoRNAs and scaRNAs. snoRNAs notably serve as adaptors for the 2'-O-methylation (2'-O-me) and pseudouridylation of ribosomal RNA (rRNA). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

20 Samples

Download data: CSV

(Submitter supplied) FUS is a nucleocytoplasmic protein involved in many processes such as RNA transport, translation, and metabolism as well as genomic maintenance. FUS mutations are found in several neurodegenerative diseases. We find that FUS knockout (KO) and FUS mutation affects the expression of many C/D box snoRNAs, H/ACA box snoRNAs and scaRNAs. snoRNAs notably serve as adaptors for the 2'-O-methylation (2'-O-me) and pseudouridylation of ribosomal RNA (rRNA).

Organism:

Homo sapiens

Type:

Other

Platform:

GPL17303

4 Samples

Download data: XLSX

(Submitter supplied) Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, transcriptome-wide measurement of individual Ψ sites remains unaddressed. Here, we develop “PRAISE”, via selective chemical labeling of Ψ by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the Ψ landscape in the human transcriptome. Unlike traditional RNA/DNA bisulfite treatment, our approach is based on quaternary base mapping and identifies 2,209 confident Ψ sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7, TRUB1 and DKC1. In addition, we identified known and novel Ψ sites in mitochondrial mRNA, which are catalyzed by a mitochondria-localized isoform of PUS1. Collectively, we provide a reliable, sensitive and convenient method to quantify transcriptome-wide Ψ; we envision this approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL11154

38 Samples

Download data: BW

(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; Nannochloropsis oculata; Arabidopsis thaliana; Triticum turgidum subsp. durum; Ginkgo biloba

Type:

Other; Non-coding RNA profiling by high throughput sequencing

6 related Platforms

14 Samples

Download data: XLS, XLSX

(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; Nannochloropsis oculata; Arabidopsis thaliana; Brassica rapa; Triticum turgidum subsp. durum; Caulerpa taxifolia

Type:

Other; Non-coding RNA profiling by high throughput sequencing

6 related Platforms

13 Samples

Download data: XLSX

(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