GEO DataSets

(Submitter supplied) Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. more...

Organism:

Bacillus cereus; Vibrio breoganii; Campylobacter jejuni; Geobacter metallireducens; Chromohalobacter israelensis

Type:

Methylation profiling by high throughput sequencing

5 related Platforms

6 Samples

Download data: CSV, GFF

(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:

synthetic construct; Caldicellulosiruptor acetigenus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19424 GPL19423

7 Samples

Download data: TSV

(Submitter supplied) NOMe-Seq analysis was performed with two cytosine C-5 DNA methyltransferases recognizing GC and CC dinucleotides were performed

Organism:

Saccharomyces cerevisiae

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17143

1 Sample

Download data: BED

(Submitter supplied) NOMe-Seq analysis was performed with GC-recognizing cytosine DNA methyltransferase

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

1 Sample

Download data: BED

(Submitter supplied) NOMe-Seq analysis was performed with CC-recognizing cytosine DNA methyltransferase

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

2 Samples

Download data: BED

(Submitter supplied) NOMe-Seq analysis was performed with two cytosine C-5 DNA methyltransferases recognizing GC and CC dinucleotides

Organism:

Saccharomyces cerevisiae

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17143

2 Samples

Download data: BED

(Submitter supplied) Bifidobacterium breve represents one of the most abundant (bifido)bacterial species in the gastro-intestinal tract of (breast-fed) infants, where their presence is believed to be beneficial. In the present study whole genome sequencing, employing PacBio’s Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. more...

Organism:

Bifidobacterium breve; Bifidobacterium breve UCC2003

Type:

Genome variation profiling by array

Platforms:

GPL8878 GPL13210

66 Samples

Download data: TXT

(Submitter supplied) Development of the human gut microbiota commences at birth with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date the genetic basis of bifidobacterial colonization and persistence remains poorly understood. Transcriptomic analysis of the 2,422,684 bp genome of Bifidobacterium breve UCC2003, a strain isolated from a nursling stool, during colonization of a mouse model revealed the differential expression of a type IVb or so-called Tad pilus-encoding cluster. more...

Organism:

Bifidobacterium breve UCC2003; Bifidobacterium breve; Mus musculus

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL13210 GPL8878

21 Samples

Download data: TXT

(Submitter supplied) Aberrant DNA methylation is frequently observed in human disease, particularly in cancer, but the underlying pathogenic mechanisms are not well understood. We demonstrate that mycoplasmal 5-methylcytosine DNA methyltransferases (MTases) can induce epigenetic alterations in human cells. We expressed the CG-specific Mhy1 and the GATC-specific Mhy2 Mycoplasma hyorhinis MTases in cultured human cells, and determined that both enzymes penetrated the cell nuclei and induced a 3.5-fold and a 2-fold increase in genome-wide methylation, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

10 Samples

Download data: TXT