GEO DataSets

(Submitter supplied) Post-transcriptional modifications of mRNA have emerged as novel regulators of gene expression. Pseudouridylation is the most abundant and widespread type of RNA modification in living organisms; however, the biological role of pseudouridine in mRNAs remains poorly understood. Here, we show that the pseudouridine synthase dyskerin associates with RNA polymerase II and is enriched at RNA polymerase II-transcribed genes genome-wide. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL21697

15 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

4 related Platforms

32 Samples

Download data: BED, BW, SF

(Submitter supplied) Post-transcriptional modifications of mRNA have emerged as novel regulators of gene expression. Pseudouridylation is the most abundant and widespread type of RNA modification in living organisms; however, the biological role of pseudouridine in mRNAs remains poorly understood. Here, we show that the pseudouridine synthase dyskerin associates with RNA polymerase II and is enriched at RNA polymerase II-transcribed genes genome-wide. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

8 Samples

Download data: BED

(Submitter supplied) Post-transcriptional modifications of mRNA have emerged as novel regulators of gene expression. Pseudouridylation is the most abundant and widespread type of RNA modification in living organisms; however, the biological role of pseudouridine in mRNAs remains poorly understood. Here, we show that the pseudouridine synthase dyskerin associates with RNA polymerase II and is enriched at RNA polymerase II-transcribed genes genome-wide. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: SF

(Submitter supplied) Dyskeratosis congenita is a bone marrow failure syndrome characterized by the presence of short telomeres at presentation. The X-linked form is caused by mutations in the gene DKC1, encoding the protein dyskerin. Dyskerin is required for in the assembly and stability of telomerase and is also involved in ribosomal RNA (rRNA) processing where it converts specific uridines to pseudouridine. DC is thought to result from failure to maintain tissues, like blood, that are renewed by stem cell activity, suggesting induced pluripotent stem (iPS) cells from X-linked DC patients may provide information about the mechanisms involved. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

6 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

27 Samples

Download data

(Submitter supplied) Total and polysomal RNA profiling of control and DKC1-silenced MCF7 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TSV

(Submitter supplied) RIP-seq of DKC1 in MCF7 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 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) Mutations in genes encoding components of the telomerase holoenzyme complex result in a spectrum of rare genetic disorders known as telomere diseases, including dyskeratosis congenita (DC). A consistent finding in DC due to pathogenic mutations in DKC1, which encodes dyskerin, is decreased steady-state levels of the non-coding RNA component of telomerase (TERC) and thus impaired telomere maintenance. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

16 Samples

Download data: FPKM_TRACKING

(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) 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) We performed pseudouridine profiling (Pseudo-seq) on 11 biological replicates of chromatin-associated RNA. We performed mRNA-seq of PUS1 knockout, PUS7 knockdown, RPUSD4 knockdown and wildtype HepG2 cells. We used an in vitro pool based strategy to assign pre-mRNA targets to individual human pseudouridine synthases (PUS) .

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

60 Samples

Download data: CSV, FASTA, TXT