GEO DataSets

(Submitter supplied) To identify HNRNPA2B1 binding sites on endogenous nuclear RNAs, we performed HITS-CLIP for endogenous HNRNPA2B1 and RNA-seq to analyze the nuclear RNA under either METTL3 or HNRNPA2B1 depletion.

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) To analyze the nuclear RNAs modified by the m6A mark

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: BED

(Submitter supplied) To identify METTL3 binding sites on endogenous nuclear RNAs, we performed HITS-CLIP endogenous METTL3

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

3 Samples

Download data: BED

(Submitter supplied) To obtain a wholistic view of hnRNP-A2B1’s role in mRNA transport in response to DNA virus infection, we profiled RNAs from nuclear and cytoplasmic fractions in both wild-type and Hnrnpa2b1–/– macrophages after Herpes simplex virus 1 (HSV-1) infection.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

4 Samples

Download data: CEL

(Submitter supplied) N6-methyladenosine (m6A) is the most common internal modification in eukaryotic messenger RNA (mRNA). The effects of this reversible cheimcal modification are mediated in part by methyl-specific RNA binding protein 'readers' of the YTH family. In this study we present the function of YTHDC1 (YT521) in promoting the export of mRNA from the nucleus to the cytoplasm. Additionally, we identify a role for YTHDC1 in exon retention in mouse embryonic stem cells (mESCs).

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL11154

38 Samples

Download data: BED, DIFF, TXT, 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) Internal modification of RNAs with N6-methyladenosine (m6A) is a highly conserved and widely used means of gene expression control. METTL16 is an m6A writer but how it recognizes its RNA targets and its physiological roles remain unknown. Here we describe the crystal structure of human METTL16 to reveal a classical methyltransferase domain but with an extra N-terminal module that is essential for catalysis. more...

Organism:

Mus musculus; synthetic RNA

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL24911

74 Samples

Download data: CSV

(Submitter supplied) N6-methyladenosine (m6A) is an abundant modification in eukaryotic mRNA, regulating mRNA dynamics by influencing mRNA stability, splicing, export and translation. Recent studies discovered m6A methyltransferases (?writer?), demethylases (?eraser?) and binding proteins (?reader?), which modulate m6A methylation. However, the precise m6A regulating machinery still remains incompletely understood. Here we demonstrate that ZC3H13, a zinc finger protein, plays an essential role in modulating m6A methylation on polyadenylated RNA in the nucleus. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21273 GPL17021

34 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) MicroRNA biogenesis is known to be modulated by a variety of RNA binding proteins (RBPs), but in most cases, individual RBPs appear to influence the processing of a small number of selective targets. We herein report binding of the NONO/PSF heterodimer to hundreds of expressed pri-miRNAs in HeLa cells to globally enhance pri-miRNA processing by the Drosha/DGCR8 Microprocessor. As NONO/PSF are key components of paraspeckles organized by the lncRNA NEAT1, we find that NEAT1 also has profound effects on global pri-miRNA processing. more...

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20301

16 Samples

Download data: BIGWIG

(Submitter supplied) m6A epitranscriptome profiling in four different chemical carcinogen induced transformation models uncovered the dynamic changes of m6A modifications during chemical carcinogenesis.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

14 Samples

Download data: BED, XLS

(Submitter supplied) Co-transcriptional processing of nascent transcripts is coupled with transcription through the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII). The mRNA modification N6-methyladenosine (m6A) occurs co-transcriptionally and impacts pre-mRNA processing. How alternative splicing of pre-mRNA is co-transcriptionally regulated in an m6A-dependent manner is not well understood. Furthermore, splicing regulation through RNAPII pausing has been frequently suggested but the underlying control mechanism remains unclear. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL20301

33 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) eCLIP-seq data of METTL3 binding in shScr control and two shDAP3 knockdown samples

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

14 Samples

Download data: XLSX

(Submitter supplied) MeRIP-seq data of m6A signals in shScr control and two shDAP3 knockdown samples

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

12 Samples

Download data: XLSX

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL21785

10 Samples

Download data: TXT

(Submitter supplied) In order to assess the possible effects of m6A on miRNA biogenesis we performed small RNA (sRNA) sequencing to compare their levels in WT Col-0 plants to those in mutant lines with severely reduced m6A levels. The reduced mta line contains MTA cDNA under the ABI3 promoter in MTA null mutant background (ABI3:MTA) and ABI3 being an embryo specific promoter rescues the embryo lethal phenotype of MTA knockout while keeping the levels of MTA in mature plants severely low34. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21785

6 Samples

Download data: TXT

(Submitter supplied) We performed m6A-RNA immunoprecipitation followed by sequencing (m6A-IP Seq) using libraries produced with unfragmented ployA+ RNA from 4 week old WT Col-0 and mta plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

4 Samples

Download data: TXT

(Submitter supplied) In order to gain insight into m6A in control and salt stress, we performed an miCLIP-sequencing experiment in control and salt treated plants

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL13222

8 Samples

Download data: NARROWPEAK

(Submitter supplied) In order to gain insight into stability of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: BED12

(Submitter supplied) In order to gain insight into abundance of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13222

50 Samples

Download data: NARROWPEAK, TXT