GEO DataSets

(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) While it has been known for several years that viral RNAs are subject to the addition of several distinct covalent modifications to individual nucleotides, collectively referred to as epitranscriptomic modifications, the effect of these editing events on viral gene expression has been controversial. Here, we report the purification of murine leukemia virus (MLV) genomic RNA to homogeneity and show that this viral RNA contains levels of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and 2’O-methylated (Nm) ribonucleotides that are an order of magnitude higher than detected on bulk cellular mRNAs. more...

Organism:

Moloney murine leukemia virus

Type:

Other

Platform:

GPL26390

9 Samples

Download data: BED

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

Organism:

Plasmodium falciparum; Plasmodium yoelii

Type:

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

Platforms:

GPL26836 GPL29225

36 Samples

Download data: XLS

(Submitter supplied) 5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. more...

Organism:

Plasmodium yoelii; Plasmodium falciparum

Type:

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

Platforms:

GPL26836 GPL29225

14 Samples

Download data: TXT, XLSX

(Submitter supplied) 5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. more...

Organism:

Plasmodium yoelii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29225

8 Samples

Download data: TXT

(Submitter supplied) 5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. more...

Organism:

Plasmodium yoelii; Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26836 GPL29225

14 Samples

Download data: TXT

(Submitter supplied) Several prior reports have demonstrated that the epitranscriptomic addition of m6A to viral transcripts promotes the replication and pathogenicity of a wide range of viruses yet the underlying mechanism(s) causing this positive effect has remained unclear. It is known that m6A function is largely mediated by cellular m6A binding proteins or readers, however, how these m6A reader proteins contribute to the regulation of HIV-1 gene expression has remained controversial. more...

Organism:

Homo sapiens; Human immunodeficiency virus 1

Type:

Other

Platform:

GPL18160

3 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

20 Samples

Download data: TXT

(Submitter supplied) To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

5 Samples

Download data: BED, TXT

(Submitter supplied) To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

3 Samples

Download data: BED, TXT

(Submitter supplied) To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

6 Samples

Download data: BED, TXT

(Submitter supplied) To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24106

6 Samples

Download data: BED, TXT

(Submitter supplied) As obligate parasites, viruses need to navigate a variety of cellular regulatory systems while infecting and replicating in the host cell. Post-transcriptional modifications have recently emerged as an important layer of regulation of viral RNA function. For example, our lab and others have shown that the RNA modification N6-methyladenosine (m6A) can enhance the replication of multiple viruses in cis, including Human Immunodeficiency virus 1 (HIV-1), Influenza A virus, SV40 and Kaposi's sarcoma-associated herpesvirus (KSHV). more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL20301 GPL18573 GPL24676

12 Samples

Download data: BED

(Submitter supplied) Cytosine-5 methylation (m5C) is one of the most prevalent modifications of RNA, playing important roles in RNA metabolism, nuclear export, and translation. However, the potential role of RNA m5C methylation in innate immunity remains elusive. Here we show that depletion of NSUN2, an m5C methyltransferase, significantly inhibits the replication and gene expression of a wide range of RNA and DNA viruses. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

44 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) 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) m6A and YTHDF1, YTHDF2, YTHDF3 mapping of IAV RNA with PAR-CLIP and pA-m6A-seq

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL11154

5 Samples

Download data: BED

(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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