GEO DataSets

(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) 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) 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) Label the cells overexpressed Flag tagged YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 with 4-SU, the RNA bound by YTHDC1 and SRSF proteins can be got by Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the 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 HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

9 Samples

Download data: CSV

(Submitter supplied) RNA was isolated from and YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 deficient human HeLa cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. 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 HiSeq2000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: 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:

GPL24676 GPL18573 GPL20301

12 Samples

Download data: BED

(Submitter supplied) The human splicing factor CRNKL1 was identified as a factor influencing splicing and/or export of the HIV RNA.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNA of all higher eukaryotes. Here we present that m6A is selectively recognized by human YTH domain family (YTHDF2) protein to regulate mRNA degradation. By using crosslinking and immunoprecipitation, we have identified over 4000 substrate RNA of YTHDF2 with conserved core motif of G(m6A)C. We further estabilshed the role of YTHDF2 in RNA metabolism by a combination of ribosome profiling, RNA sequencing, m6A level quantification and cell-based imaging: the C-terminal domain of YTHDF2 selectively binds to m6A of mRNA and the N-terminal domain is responsive for localizing mRNA from translatable pool to processing body where mRNA decay occurs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

29 Samples

Download data: XLSX

(Submitter supplied) N6-methyladenosine (m6A) is the most prevalent internal modification found in mammalian messenger and non-coding RNAs. The discoveries of functionally significant demethylases that reverse this methylation as well as the recently revealed m6A distributions in mammalian transcriptomes strongly indicate regulatory functions of this modification. Here we report the identification and characterization of the mammalian nuclear RNA N6-adenosine methyltransferase core (RNMTC) complex. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

32 Samples

Download data: CSV, TXT

(Submitter supplied) The internal N6-methyladenosine (m6A) methylation of eukaryotic nuclear RNA controls post-transcriptional gene expression, which is regulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers) in cells. The YTH domain family proteins (YTHDF1–3) bind to m6A-modified cellular RNAs and affect RNA metabolism and processing. Here, we show that YTHDF1–3 proteins recognize m6A-modified HIV-1 RNA and inhibit HIV-1 infection in cell lines and primary CD4+ T-cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: BED

(Submitter supplied) As the crucial m6A reader, YTHDF2 usually degrades the target mRNAs by recognizing the m6A modified sites, consequently altering m6A levels of each mRNA. In this study, we used m6A MeRIP sequencing to detect the m6A modification alterations in prostate cancer (PCa) cell line after knocking down YTHDF2 and identify how YTHDF2 promote the PCa progression by mediating the mRNA degradation in m6A-dependent way.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Other

Platform:

GPL20301

12 Samples

Download data: WIG

(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) The m6A methylation pathway has previously been shown to influence pluripotency. YTHDF2 is an RNA binding protein that interacts with m6A-modified RNAs to facilitate their degradation. We sought to identify the cohort of RNAs targeted by YTHDF2 in human induced pluripotent stem cells (iPSC).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: FASTA, GTF, TDF, TXT, XLSX

(Submitter supplied) N6-methyladenosine (m6A) on chromosome-associated regulatory RNAs (carRNAs), including repeat RNAs, plays important roles in tuning the chromatin state and transcription, but the intrinsic mechanism remains unclear. Here, we report that YTHDC1 plays indispensable roles in the embryonic stem cell (ESC) self-renewal and differentiation potency, which highly depends on its m6A-binding ability. Ythdc1 is required for sufficient rRNA synthesis and repression of the 2-cell transcriptional program in ESCs, which recapitulates the transcriptome regulation by the LINE1 scaffold. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: FPKM_TRACKING

(Submitter supplied) N6-methyladenosine (m6A) on chromosome-associated regulatory RNAs (carRNAs), including repeat RNAs, plays important roles in tuning the chromatin state and transcription, but the intrinsic mechanism remains unclear. Here, we report that YTHDC1 plays indispensable roles in the embryonic stem cell (ESC) self-renewal and differentiation potency, which highly depends on its m6A-binding ability. Ythdc1 is required for sufficient rRNA synthesis and repression of the 2-cell transcriptional program in ESCs, which recapitulates the transcriptome regulation by the LINE1 scaffold. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: BW