Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping replication domains using the Ion Torrent semiconductor sequencing platform [BrdU-IP]

ABSTRACT: We show that semiconductor-based sequencing technology can be used to map mammalian replication domains, chromosomal units with similar DNA replication timing. Replicating DNA purified from mammalian cells was successfully sequenced by the Ion Torrent platform. The resultant replication domain map of mouse embryonic cells is comparable to those obtained by the conventional microarray-based method.

ORGANISM(S): Mus musculus

PROVIDER: GSE115847 | GEO | 2018/10/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Mapping replication domains using the Ion Torrent semiconductor sequencing platform [BrdU-IP]

Project description:Mapping replication domains using the Ion Torrent semiconductor sequencing platform [BrdU-IP]

| PRJNA476299 | ENA

Semiconductor based DNA sequencing of histone modification states

Project description:The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here, we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumor tissues.

2013-10-25 | GSE49477 | GEO

Semiconductor based DNA sequencing of histone modification states

2013-10-25 | E-GEOD-49477 | biostudies-arrayexpress

Semiconductor-based sequencing of genome-wide DNA methylation states

Project description:Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we present a novel MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is scalable and accurately identifies sites of differential DNA methylation. Additionally, we demonstrate that the high-throughput data derived from MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450K Beadchip array. We applied this integrative approach to further investigate the role of DNA methylation in alternative splicing and to profile 5-mC and 5-hmC variants of DNA methylation in normal human brain tissue that we observed localize over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions. MeDIP-Seq on Ion Torrent Platform in HCT116 and Human Brain

2015-06-10 | E-GEOD-61968 | biostudies-arrayexpress

Semiconductor-based sequencing of genome-wide DNA methylation states

2015-06-10 | GSE61968 | GEO

MC Ion Torrent Nextera 500pg

Project description:MC Ion Torrent Nextera 500pg Synthetic Metagenome

| PRJNA172891 | ENA

MC Ion Torrent Nextera 50ng

Project description:MC Ion Torrent Nextera 50ng Synthetic Metagenome

| PRJNA172890 | ENA

MC Ion Torrent Standard 500ng

Project description:MC Ion Torrent Standard 500ng Synthetic Metagenome

| PRJNA172889 | ENA