GEO DataSets

(Submitter supplied) Here, we use a novel technique for locating regions of N6-adenosine methylation (m6A) throughout the transcriptome and present a profile of m6A sites in the mouse brain. Our use of methylated RNA immunoprecipitation combined with RNA-seq (MeRIP-Seq) identifies thousands of RNAs which contain m6A sites. In addition, we find that regions of m6A formation are particularly enriched near stop codons, which might provide clues into the potential funciton of this highly prevalent RNA modificaiton.

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL13112 GPL11002 GPL11154

11 Samples

Download data: BW, TXT

(Submitter supplied) N1-Methyladenosine (m1A) is a prevalent post-transcriptional RNA modification, yet little is known about its abundance, topol- ogy and dynamics in mRNA. Here, we show that m1A is prevalent in Homo sapiens mRNA, which shows an m1A/A ratio of ~0.02%. We develop the m1A-ID-seq technique, based on m1A immunoprecipitation and the inherent ability of m1A to stall reverse tran- scription, as a means for transcriptome-wide m1A profiling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

24 Samples

Download data: TXT

(Submitter supplied) m6A profiling in two accessions of Arabidopsis thaliana (Can-0 and Hen-16) using the m6A-targeted antibody coupled with high-throughput sequencing

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: TDF

(Submitter supplied) We used DART-seq to map m6A methylation of RNA in single HEK293T cells. We also used DART-seq to map m6A from bulk RNA from HEK293T cells. Using the 10X Genomics and SMART-seq2 platforms, we sequenced a total of 19,533 experimental and control cells using the 10X Genomics platform, and 1,471 experimental and control cells using SMART-seq2. We then used a Bullseye, a computational pipeline developed within the lab, to identify m6A sites from the C-to-U mutations in bulk and single-cell datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1681 Samples

Download data: BED

(Submitter supplied) We report m6Am-seq, based on selective in vitro demethylation and RNA immunoprecipitation. m6Am-seq directly distinguishes m6Am and 5’-UTR N6-methyladenosine (m6A).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20795

34 Samples

Download data: BW, CSV

(Submitter supplied) Background: Hepatic ischemia reperfusion injury (IRI) is a complex clinical complication during surgery and often leads to cell damage and dysfunction. N6-Methyladenosine (m6A) is an emerging epigenetic modification that plays key roles in the regulation of biological functions and cellular mechanisms in IR injury in different organs. However, the understanding of m6A-modified mRNAs in hepatic IRI is limited. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

20 Samples

Download data: BEDGRAPH

(Submitter supplied) By adapting UV cross-linking immune precipitation for m6A (m6A-CLIP), we developed several novel genomic approaches with single-nucleotide resolution to accurately locate tens of thousands of m6A residues in human cells and mouse brain mRNAs. We found over 70% of these residues in the last exon with a very sharp rise (six-fold) within 150-400 nucleotides of the last exon, which overlaps the beginning of many 3′ untranslated region (UTRs). more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

4 related Platforms

8 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish 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 HiSeq2500 or HiSeq 3000 (Illumina) in paired-read mode, creating reads with a length of 101 or 151 bp. more...

Organism:

Danio rerio

Type:

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

Platforms:

GPL23274 GPL18413

18 Samples

Download data: XLS

(Submitter supplied) We performed RNA sequencing (RNA-seq) and m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in control and Zfp217 knockout 3T3L1 cells with MDI treatment for 0d and 2d Loss-of-function study demonstrates that Zfp217 deficiency impaired adipogenesis together with a global increase of m6A modification in 3T3L1cells. To gain an overview of the global role of Zfp217 in adipogenesis, we performed RNA sequencing (RNA-seq) in control and Zfp217 knockout 3T3L1 cells with MDI treatment for 0d and 2d and identified 12,188 and 11,566 different expressed genes (DEG) for 0d and 2d, respectively. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

36 Samples

Download data: TXT, XLSX

(Submitter supplied) m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, m6A differential patterns among organs have not been well characterized. The goal of the study is to comprehensively analyze m6A patterns of numerous types of RNAs, the relationship between transcript level and m6A methylation extent, and m6A differential patterns among organs in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13222

18 Samples

Download data: BEDGRAPH

(Submitter supplied) In this experiment, we constructed a mouse myocardial hypertrophy model through transverse aortic constriction (TAC) to further explore the relationship between m6A modification and myocardial hypertrophy, MeRIP-seq and RNA-seq were performed to identify genes with differences m6A modification or expression in transcriptome profile.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

12 Samples

Download data: XLSX

(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) Methylation is the most common internal modification in mRNA. While the highly abundant N6-methyladonsine (m6A) modification affects most aspects of mRNA function, the precise functions of the rarer 5-methylcytosine (m5C) remains largely unknown. Here, we map m5C in the human transcriptome using methylation-dependent individual-nucleotide resolution cross-linking and immunoprecipitation (miCLIP) combined with RNA bisulfite sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL9115

61 Samples

Download data: BED, TXT

(Submitter supplied) Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region readthrough allows translation into the mRNA 3’-UTR. more...

Organism:

Saccharomyces cerevisiae W303

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL27477

16 Samples

Download data: TXT

(Submitter supplied) N7-methylguanosine (m7G) is a positively charged, essential modification at the 5′ cap of eukaryotic mRNA, regulating mRNA export, translation, and splicing. m7G also occurs internally within tRNA and rRNA, but its existence and distribution within eukaryotic mRNA remain to be investigated. Here, we show the presence of internal m7G sites within mammalian mRNA. We then performed transcriptome-wide profiling of internal m7G methylome using m7G-MeRIP sequencing (MeRIP-seq). more...

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL19057 GPL20301

104 Samples

Download data: BED, FPKM_TRACKING, TXT, XLSX

(Submitter supplied) Purpose: To transcriptome widely reveal 5-mC regulation by Tet2, we performed bisulfite-sequencing of mRNAs from Tet2-deficient BMMCs and the control cells.Methods: Mouse BMMCs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse IL-3 and SCF. BMMCs were stained to confirm the surface expression of FcɛRI and c-Kit. Cells with purity >97.5% were used for RNA isolation. Results: We carried out an unbiased global analysis of m5C in poly(A)RNA of mouse bone marrow derived mast cells (BMMCs).We show that there were indeed much more mCs in Tet2-deficient group compared with the control, more than half of which located in genic region. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21273

8 Samples

Download data: TXT

(Submitter supplied) Purpose:The purpose of this study is to detect activated or silenced genes during Tet2-deficient bone marrow derived mast cell (BMMC) and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods:Mouse BMMCs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse IL-3 and SCF. BMMCs were stained to confirm the surface expression of FcɛRI and c-Kit. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

2 Samples

Download data: TXT

(Submitter supplied) To transcriptome-widely identify the mRNA targets of Tet2 and investigate the immunological function of Tet2 at RNA regulation level in vivo, we performed CLIP-seq of Tet2 in BMMCs. We performed three bio-replicates of CLIP-seq for getting potential Tet2-binding mRNAs.Using data of normalized tag numbers in the common peaks, we found that biological replicates correlated well with each other.More than 60% of the peaks located in genic regions, which were preferentially enriched in coding sequencing (CDS) among mature mRNA elements.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21493

3 Samples

Download data: TXT

(Submitter supplied) Apolipoprotein B-editing enzyme, catalytic polypeptide-1 (APOBEC1) is a cytidine deaminase, initially identified by its activity in converting a specific cytidine (C) to uridine (U) in apolipoprotein B (apoB) mRNA transcripts in the small intestine. Editing results in translation of a truncated apoB isoform with distinct functions in lipid transport. To address the possibility that APOBEC1 edits additional mRNAs, we developed a transcriptome-wide comparative RNA-Seq screen. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BAM

(Submitter supplied) N6-methyladenosine RNA (m6A) is the most abundant modification of messenger RNA (mRNA), which has been demonstrated in regulating various post-transcriptional processes and playing key roles in sex determination, neuronal functions, and embryonic development in Drosophila and mice. However, the methylation profile and relevant functions in other insects remain largely unknown. Here, we analyzed transcriptome-wide profile of m6A modification in the embryonic development of a destructive agricultural pest Spodoptera frugiperda. more...

Organism:

Spodoptera frugiperda

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29193

12 Samples

Download data: BED