GEO DataSets

(Submitter supplied) We generated a map of NSUN6-dependent RNA 5 methyl-cytosine in the human transcriptome by applying RNA bisulfite conversion and sequencing to two sets of cell lines (HUES9 and HEK293) where the RNA cytosine 5 methyl-transfearse NSUN6 has been either knocked out by CRISPR Cas9 or overexpressed using a PiggyBac vector. We apply this and other molecular methods to validate NSUN6 RNA methylation targets with single nucelotide resolution in the human transcriptome.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL16791 GPL20301

68 Samples

Download data: COV

(Submitter supplied) Human keratinocytes were cultured either as undifferentiated or differentiated cells. Total RNA extracted from both conditions and depleted from rRNA then treated with three cycles of Sodium bisulfite. DNA libraries were then generated from converted RNA for sequecing.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: COV

(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) The 5-methylcytosine (m5C) modification is present at appreciable amounts in the mammalian transcriptome, but its precise location and function is still poorly understood. Here, we identify high m5C levels and map their locations in a model retrovirus, the murine leukemia virus, and show that the ALYREF m5C reader protein regulates viral replication. Our results reveal a single-nucleotide m5C profile in a virus and its function in a eukaryotic mRNA.

Organism:

Mus musculus; Murine leukemia virus

Type:

Other

Platforms:

GPL27704 GPL27705

4 Samples

Download data: TXT

(Submitter supplied) In this GEO submission we include the PA-m6A-seq and PA-m5C-seq datasets for HIV in CEM & 293T cells

Organism:

Human immunodeficiency virus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26648

11 Samples

Download data: BED

(Submitter supplied) Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology and development. The goal of this study is to establish how tRNA-derived small RNAs can affect stem cell function. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

11 Samples

Download data: TXT

(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

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

4 related Platforms

44 Samples

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(Submitter supplied) RNA was isolated from siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) or HiSeq2500 in paired-read mode, creating reads with a length of 101 or 125 bp. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL21493 GPL21290

22 Samples

Download data: XLS

(Submitter supplied) mRNAs of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement. mRNAs were fragmented to ~200 nt and treated by Sodium bisulfite solution (pH 5.1) containing Hydroquinone. Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2500 (Illumina) in pair-end mode, creating reads with a length of 125 bp. more...

Organism:

Mus musculus; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

22 Samples

Download data: XLS

(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

(Submitter supplied) A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here we identify Serine/arginine-Rich Splicing Factor 2 (SRSF2) as a reader of m5C, and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and in the impact of the prevalent leukemia-associated mutation SRSF2P95H. more...

Organism:

Homo sapiens

Type:

Other; Methylation profiling by high throughput sequencing

4 related Platforms

38 Samples

Download data: BED, BEDGRAPH, TSV, TXT

(Submitter supplied) We report on how the loss of vtRNA1.1 reshapes the transcriptome in starved Hela cells. We observe misregulated transcript levels for proteins involved in cellular signaling cascades.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

24 Samples

Download data: XLSX

(Submitter supplied) 5-methylcytosine sites of mRNA in BxPC-3, PANC1, and MiaPaCa-2 pancreatic cancer cells at the single-base resolution by whole-transcriptome bisulfite sequencing.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Other

Platform:

GPL18573

15 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 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; Ginkgo biloba; Arabidopsis thaliana; Triticum turgidum subsp. durum

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

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

(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