GEO DataSets

(Submitter supplied) In cell biology, ribosomal RNA (rRNA) 2'O-methyl (2'-O-Me) is the most prevalent post-transcriptional chemical modification contributing to ribosome heterogeneity. The modification involves a family of small nucleolar RNAs (snoRNAs) and is specified by box C/D snoRNAs (SNORDs). Given the importance of ribosome biogenesis for skeletal muscle growth, we asked if rRNA 2'-O-Me in nascent ribosomes synthesized in response to a growth stimulus is an unrecognized mode of ribosome heterogeneity in muscle. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL18635

4 Samples

Download data: XLSX

(Submitter supplied) A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was applied to study methylation patterns in Dictyostelium discoideum

Organism:

Dictyostelium discoideum

Type:

Other

Platform:

GPL30893

2 Samples

Download data: XLSX

(Submitter supplied) Transcriptome analysis of skeletal muscle during hypertrophic growth in aged mice Global gene expression patterns were determined from microarray results on day 1, 3, 5, 7, 10 and 14 during plantaris muscle hypertrophy induced by synergist ablation in old adult mice (25 months).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

14 Samples

Download data: CEL, CHP

(Submitter supplied) Global gene expression patterns were determined from microarray results on day 1, 3, 5, 7, 10 and 14 during plantaris muscle hypertrophy induced by synergist ablation in young adult mice (5 months).

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4932

Platform:

GPL6246

14 Samples

Download data: CEL

Analysis of right and left plantaris muscle from young males (5 months old) subjected to 1, 3, 5, 7, 10 and 14 days of synergist ablation surgery to induce hypertrophy. Results provide insight into the molecular response of young skeletal muscle to mechanical overload induced by synergist ablation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 stress, 7 time, 2 tissue sets

Platform:

GPL6246

Series:

GSE47098

14 Samples

Download data: CEL

(Submitter supplied) A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns during Zebrafish (Danio rerio) development

Organism:

Danio rerio

Type:

Other

Platforms:

GPL24059 GPL28630

18 Samples

Download data: FA, XLSX

(Submitter supplied) Ribose methylation is one of the two most abundant modifications in human ribosomal RNA and is believed to be important for ribosome biogenesis, mRNA selectivity and translational fidelity. We have applied RiboMeth-seq to rRNA from HeLa cells for ribosome-wide, quantitative mapping of 2'-O-Me sites and obtained a comprehensive set of 106 sites, including two novel sites, and with plausible box C/D guide RNAs assigned to all but three sites. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17303

3 Samples

Download data: XLSX

(Submitter supplied) The 2’-O-methylation (2’-O-Me) of ribosomal RNA (rRNA) shows plasticity potentially associated with specific cell phenotypes. We used RiboMeth-seq profiling to reveal senescence- and proliferation-specific 2’-O-Me patterns in stress induced premature senescent (SIPS) human dermal fibroblasts.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: XLSX

(Submitter supplied) Ribosomes are the macromolecular engines of protein synthesis. Factors mediating ribosome biogenesis in skeletal muscle that facilitate adaptation to exercise are multi-factorial, but may be related to ribosomal DNA (rDNA) dosage and/or epigenetic modifications to rDNA. To investigate these possibilities, we conducted reduced representation bisulfite sequencing (RRBS) on skeletal muscle biopsies from human subjects before and after exercise and to detect differences in methylation patterns during exercise adaptation.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

33 Samples

Download data: COV

(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) Ribosomal RNAs (rRNAs) are main effectors of mRNA decoding, peptide-bond formation and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and display a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TSV

(Submitter supplied) RNA helicases play important roles in diverse aspects of RNA metabolism through their functions in remodelling ribonucleoprotein complexes (RNPs), such as pre-ribosomes. Here, we show that the DEAD box helicase Dbp3 is required for efficient processing of the U18 and U24 intron-encoded snoRNAs and 2'-O-methylation of various sites within the 25S ribosomal RNA (rRNA) sequence. Furthermore, numerous box C/D snoRNPs accumulate on pre-ribosomes in the absence of Dbp3. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL18249

8 Samples

Download data: XLSX

(Submitter supplied) We conducted reduced representation bisulfite sequencing (RRBS) on myonuclei and interstitial nuclei and observed stark differences in methylation patterns during adaptation

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: BW

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

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25244 GPL30203

46 Samples

Download data: CSV, TXT

(Submitter supplied) The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). We built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing (TGIRT-seq).

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL30203

34 Samples

Download data: CSV

(Submitter supplied) The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). We built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing (TGIRT-seq).

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

6 Samples

Download data: TXT