GEO DataSets

(Submitter supplied) We present a chemical method (m6A-ORL-Seq) for transcriptome-wide m6A profiling , and compared its results with MeRIP-seq.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

7 Samples

Download data: BED

(Submitter supplied) Here we report a metabolic labeling method to map mRNA N6-methyladenosine (m6A) modification transcriptome-wide at base resolution, termed m6A-label-seq. The cells were fed with Se-allyl-L-selenohomocysteine, an analog of methoine, which serves as the precursor of methylation enzyme cofactor, so that cellular RNAs were continuously deposited with N6-allyladenosine (a6A) at supposed m6A sites. We enriched a6A-containing mRNAs and sequenced their a6A sites which are identical to m6A sites, based on iodination-induced misincorporation during reverse transcription.

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL20795 GPL21273

17 Samples

Download data: BED, TXT, XLS, XLSX

(Submitter supplied) We introduce m6A Selective Allyl Chemical labeling and Sequencing (m6A-SAC-Seq), a novel method for transcriptome-wide quantitative mapping of m6A at single-nucleotide resolution. The m6A-SAC-Seq employs a dimethyltransferase to selectively label m6A followed by introducing mutations with reverse transcriptase during sequencing. We identified the widespread distributions of m6A and quantitated their fractions in the transcriptome of HeLa, HEK293, HepG2, and human CD34+ hematopoietic stem/progenitor cells (HSPCs).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

55 Samples

Download data: TSV

(Submitter supplied) We introduce m6A Selective Allyl Chemical labeling and Sequencing (m6A-SAC-Seq), a novel method for transcriptome-wide quantitative mapping of m6A at single-nucleotide resolution. The m6A-SAC-Seq employs a dimethyltransferase to selectively label m6A followed by introducing mutations with reverse transcriptase during sequencing. We identified the widespread distributions of m6A and quantitated their fractions in the transcriptome of HeLa, HEK293, HepG2, and human CD34+ hematopoietic stem/progenitor cells (HSPCs).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

22 Samples

Download data: BED

(Submitter supplied) We introduce m6A Selective Allyl Chemical labeling and Sequencing (m6A-SAC-Seq), a novel method for transcriptome-wide quantitative mapping of m6A at single-nucleotide resolution. The m6A-SAC-Seq employs a dimethyltransferase to selectively label m6A followed by introducing mutations with reverse transcriptase during sequencing. We identified the widespread distributions of m6A and quantitated their fractions in the transcriptome of HeLa, HEK293, HepG2, and human CD34+ hematopoietic stem/progenitor cells (HSPCs).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

29 Samples

Download data: BED

(Submitter supplied) We applied chemical-assisted, m6A-SEAL method to profile m6A distributions in the transcriptomes of human and plant cells and compared its results against MeRIPm6A-seq.

Organism:

Oryza sativa; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL21087 GPL20795 GPL24468

16 Samples

Download data: BW

(Submitter supplied) We report evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology for quantitative, base-resolution profiling of m6A. eTAM-seq functions by global adenosine deamination, enabling detection of m6A as persistent A. We demonstrate adenosine-to-inosine (I) conversion rates up to 99% using a hyperactive TadA variant. With eTAM-seq, we profile and quantify m6A in the whole transcriptomes of HeLa cells and mouse embryonic stem cells (mESCs), with simultaneous deconvolution of the transcriptome and epitranscriptome. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL24247

19 Samples

Download data: TXT

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

Organism:

Mus musculus; Escherichia coli; synthetic construct; Homo sapiens

Type:

Other

5 related Platforms

83 Samples

Download data

(Submitter supplied) We report evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology for quantitative, base-resolution profiling of m6A. eTAM-seq functions by global adenosine deamination, enabling detection of m6A as persistent A. We demonstrate adenosine-to-inosine (I) conversion rates up to 99% using a hyperactive TadA variant. With eTAM-seq, we profile and quantify m6A in the whole transcriptomes of HeLa cells and mouse embryonic stem cells (mESCs), with simultaneous deconvolution of the transcriptome and epitranscriptome. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

50 Samples

Download data: XLSX

(Submitter supplied) We report evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology for quantitative, base-resolution profiling of m6A. eTAM-seq functions by global adenosine deamination, enabling detection of m6A as persistent A. We demonstrate adenosine-to-inosine (I) conversion rates up to 99% using a hyperactive TadA variant. With eTAM-seq, we profile and quantify m6A in the whole transcriptomes of HeLa cells and mouse embryonic stem cells (mESCs), with simultaneous deconvolution of the transcriptome and epitranscriptome. more...

Organism:

Escherichia coli; synthetic construct

Type:

Other

Platforms:

GPL16085 GPL17769

14 Samples

Download data: XLSX

(Submitter supplied) We report RBS-Seq, a new RNA bisulfite sequencing method enabling the sensitive and simultaneous detection of m5C, pseudouridine, and m1A at single-base resolution transcriptome-wide. For each, we detect ‘signature’ base mismatches (for m5C and m1A), or 1-2 base deletions (for pseudouridine) structurally explained by ribose ring-opened pseudouridine-mono-bisulfite adducts.  Our profiles for pseudouridine reveal clear signatures at known sites in tRNAs and rRNAs, and provide hundreds of new targets in non-coding RNAs and mRNAs. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL15520

14 Samples

Download data: XLSX

(Submitter supplied) tRNAs are subject to numerous modifications including methylation. Mutations in the human N7-methylguanosine (m7G) methyltransferase complex METTL1-WDR4 cause primordial dwarfism and brain malformation yet the molecular and cellular function in mammals is not well understood. We developed m7G methylated tRNA immunoprecipitation sequencing (MeRIP-Seq) and tRNA reduction and cleavage sequencing (TRAC-Seq) to reveal the m7G tRNA methylome in mouse embryonic stem cells (mESCs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

26 Samples

Download data: TXT

(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) 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:

GPL19057 GPL18573 GPL20301

104 Samples

Download data: BED, FPKM_TRACKING, TXT, XLSX

(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) Chemical modifications on mRNA are increasingly recognized as a critical regulatory layer of the flow of genetic information, but quantitative tools to monitor RNA modifications in a whole-transcriptome and site-specific manner are lacking. Here we describe a versatile directed evolution platform that rapidly selects for reverse transcriptases that install mutations during reverse transcription at sites of a given type of RNA modification, allowing for site-specific identification of the modification. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N1-methyladenosine (m1A) is a recently identified mRNA modification; however, little is known about its precise location, regulation and function. Here, we develop a single-nucleotide resolution m1A profiling method, based on m1A-induced misincorporation during reverse transcription, and report distinct classes of m1A methylome in the human transcriptome. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

24 Samples

Download data: TXT

(Submitter supplied) m6A is a widespread RNA modification which plays important roles in the regulation of gene expression. Methods for the global detection of m6A rely on immunoprecipitation of methylated transcripts using m6A antibodies. However, these methods are costly and require large amounts of input RNA, making them prohibitive for many experiments. Here, we describe DART-seq, an antibody-free method for m6A detection which enables transcriptome-wide mapping of m6A residues using low amounts of input material. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL20301 GPL19124

11 Samples

Download data: BED

(Submitter supplied) we profiled the transcriptome-wide m6A modification in lncRNAs and circRNA in MDV-infected chicken embryo fibroblast (CEF) cells. Methylated RNA immunoprecipitation sequencing results revealed that the lncRNA m6A modification is highly conserved with MDV infection increasing the expression of lncRNA m6A modified sites compared to uninfected cell controls. m6A modification was highly conserved in circRNAs. more...

Organism:

Gallus gallus

Type:

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

Platform:

GPL23499

12 Samples

Download data: BED, XLSX