GEO DataSets

(Submitter supplied) DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. more...

Organism:

Escherichia coli; Oxytricha trifallax

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL30646 GPL21222

10 Samples

Download data: CSV, TXT

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

Organism:

Helicobacter pylori; mixed culture metagenome; Escherichia coli; Oxytricha trifallax

Type:

Methylation profiling by high throughput sequencing; Other

4 related Platforms

22 Samples

Download data: CSV, TXT

(Submitter supplied) DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. more...

Organism:

Helicobacter pylori; Escherichia coli; mixed culture metagenome

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL21222 GPL30645 GPL30644

14 Samples

Download data: CSV

(Submitter supplied) N4-methylcytosine is a major DNA modification integral to restriction-modification (R-M) systems in bacterial genomes. Here we describe 4mC-Tet-Assisted Bisulfite-sequencing (4mC-TAB-seq), a method that accurately and rapidly reveals the genome-wide locations of N4-methylcytosines at single-base resolution. By coupling Tet-mediated oxidation with a modified sodium bisulfite conversion reaction, unmodified cytosines and 5-methylcytosines are read out as thymines, whereas N4-methylcytosines are read out as cytosines revealing their positions throughout the genome.

Organism:

Caldicellulosiruptor acetigenus; synthetic construct

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19424 GPL19423

7 Samples

Download data: TSV

(Submitter supplied) We report the application of SMRT seqeuncing from Pacific Biosciences to study the DNA base modifications in dam-/dcm- and wild type E.coli.

Organism:

Escherichia coli

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24462

2 Samples

Download data: GFF

(Submitter supplied) DNA methylation is a key mechanism for regulation of DNA repair, DNA replication, and gene expression. In bacteria, DNA is modified by methylation on C5-cytosine (5mC), N6-adenine (6mA) and N4-cytosine (4mC). Metazoans were thought to only use 5mC to regulate gene expression until the recent discovery of N6-adenine methylation in DNA of diverse metazoan species, including mammals. Here we show by dot blot, immunoprecipitation with 4mC-specific antibodies, and ultra-high performance liquid chromatography coupled with triple-quadrupole mass spectrometry that 4mC also occurs in most eukaryotes. more...

Organism:

Caenorhabditis elegans

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19919

1 Sample

Download data: GFF

(Submitter supplied) In mammalian cells, DNA methylation on the 5th position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N6-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. more...

Organism:

Caenorhabditis elegans

Type:

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

Platforms:

GPL19919 GPL18245

3 Samples

Download data: BW, GFF, NARROWPEAK

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing

Platforms:

GPL13534 GPL16791 GPL20795

19 Samples

Download data: BED, BW, IDAT

(Submitter supplied) The gold standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC, however new approaches to map 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC. In this study, we provide a comparative analysis on brain DNA using three 5hmC genome-wide approaches; namely whole-genome bisulphite/oxidative-bisulphite sequencing (WG Bis/OxBis-seq), Infinium HumanMethylation450 BeadChip arrays coupled with oxidative bisulphite (HM450K Bis/OxBis) and antibody-based immunoprecipitation and sequencing of hydroxymethylated DNA (hMeDIP-seq). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

5 Samples

Download data: BED, BW

(Submitter supplied) The gold standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC, however new approaches to map 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC. In this study, we provide a comparative analysis on brain DNA using three 5hmC genome-wide approaches; namely whole-genome bisulphite/oxidative-bisulphite sequencing (WG Bis/OxBis-seq), Infinium HumanMethylation450 BeadChip arrays coupled with oxidative bisulphite (HM450K Bis/OxBis) and antibody-based immunoprecipitation and sequencing of hydroxymethylated DNA (hMeDIP-seq). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TSV

(Submitter supplied) The gold standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC, however new approaches to map 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC. In this study, we provide a comparative analysis on brain DNA using three 5hmC genome-wide approaches; namely whole-genome bisulphite/oxidative-bisulphite sequencing (WG Bis/OxBis-seq), Infinium HumanMethylation450 BeadChip arrays coupled with oxidative bisulphite (HM450K Bis/OxBis) and antibody-based immunoprecipitation and sequencing of hydroxymethylated DNA (hMeDIP-seq). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

8 Samples

Download data: IDAT

(Submitter supplied) N 4-methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) method for genome-wide mapping of 4mC at single-base resolution. more...

Organism:

Deinococcus radiodurans

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL31018

3 Samples

Download data: CSV

(Submitter supplied) We describe the development and thorough validation of a new approach for epigenome analysis (named TOP-seq) that is based on a novel concept – combination of selective covalent tagging and targeted genomic sequencing of the genome. The technique reports the modification status of each genomic CpG site by priming the DNA polymerase action from a tethered oligonucleotide probe that is selectively attached to the unmodified CpG sites.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17303

19 Samples

Download data: BEDGRAPH

(Submitter supplied) Purpose and methods:Transcriptome profiling of Phytophthora sojae P6497 mycelium (3-days old) and Phytophthora infestans T30-4 mycelium (6-days old) were generated to find out the relationship between 6mA methylation and gene expression. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiling of P. sojae psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was generated to check the differential expressed genes (DEGs) between the mutant and wild-type P. more...

Organism:

Phytophthora sojae; Phytophthora infestans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25218 GPL25217

7 Samples

Download data: GTF, XLSX

(Submitter supplied) We report the 6mA methylation profiling in two Phytophthora species and one psdamt3 mutant. Genomic DNA of Phytophthora sojae P6497 mycelium (3-days old), Phytophthora infestans T30-4 mycelium and psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was extracted and sonicated to 200-400bp using Biorupter UCD-600. The antibody sysy 202003 was used to immunoprecipitation. We find that 6mA is associated with lowly expressed genes in two Phytophthora species. more...

Organism:

Phytophthora sojae; Phytophthora infestans

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL25217 GPL25218

12 Samples

Download data: BED

(Submitter supplied) DNA methylation 5mC specific detection has been limited by the mixed signals from traditional bisulfite sequencing or by the severe degradation of input during oxBS-seq pretreatment. Here, we presented a 5mC specific whole genome amplification method (5mC-WGA), with which we achieved whole genome bisulfite sequencing with 5mC retention from limited input down to 10 pg scale without 5hmC signals, presenting DNA 5mC methylome with high producibility and great accuracy.

Organism:

Mus musculus; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

15 Samples

Download data: COV

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

Organism:

Adineta vaga

Type:

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

Platforms:

GPL27729 GPL27727 GPL27728

17 Samples

Download data: BED, BW

(Submitter supplied) Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. more...

Organism:

Adineta vaga

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27729 GPL27727

5 Samples

Download data: FASTA, GFF3, TXT

(Submitter supplied) Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. more...

Organism:

Adineta vaga

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27728

4 Samples

Download data: BED, BW

(Submitter supplied) Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. more...

Organism:

Adineta vaga

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27727

8 Samples

Download data: BED