Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mixed culture

ABSTRACT: Ion Torrent Bias Experiment

PROVIDER: PRJNA167265 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR515922.fastq.gz	Fastqsanger.gz
	SRR515923.fastq.gz	Fastqsanger.gz
	SRR515924.fastq.gz	Fastqsanger.gz
	SRR515925.fastq.gz	Fastqsanger.gz
	SRR515926.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 31

Similar Datasets

Evaluating bias-reducing protocols for RNA sequencing library preparation

Project description:The ligation step in RNA sequencing library generation is a known source of bias. We present the first comparison of the standard duplex adaptor protocol supplied by Life Technologies for use on the Ion Torrent PGM with an alternate single adaptor approach involving CircLigase (CircLig). We also investigate whether using the thermostable ligase Methanobacterium thermoautotrophicum RNA ligase K97A (Mth K97A) for the initial ligation step in the CircLigase protocol reduces bias. A pool of small RNA fragments of known composition was converted into a sequencing library using one of three protocols and sequenced on an Ion Torrent PGM. The single adaptor CircLigase-based approach significantly reduces, but does not eliminate, bias in Ion Torrent data. Using Mth K97A as part of the CircLig method does not further reduce bias.

2014-06-24 | E-MTAB-2566 | biostudies-arrayexpress

MicroRNA sequencing of mouse soleus muscle

Project description:MicroRNA sequencing using Ion Torrent Proton platform

2015-03-31 | GSE63342 | GEO

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

mixed culture metagenome

Project description:Quantifying Bias in 16S rRNA Experiments due to DNA Extraction, PCR Amplification, and Sequencing and Classification

| PRJNA267701 | ENA

Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-RRBS

Project description:We describe XmaI-RRBS method for rapid and affordable genome-wide DNA methylation analysis, with library preparation taking only four days and sequencing possible within four hours. Small sizes of the XmaI-RRBS libraries allow their multiplexing and sequencing on the benchtop high-throughput machines. Described here is the first RRBS protocol validated for the Ion Torrent Personal Genome Machine. DNA from MCF7 cell line and 6 normal breast samples (total 7 samples) were subjected to reduced representation bisulfite sequencing analysis (XmaI-RRBS) by using Ion Torrent platform.

2015-11-01 | E-GEOD-74126 | biostudies-arrayexpress

MicroRNA sequencing and analysis of the newt heart

Project description:MicroRNA sequencing using Ion Torrent Proton platform of the undamaged heart of the red spotted newt Notophthalmus viridescens. MicroRNAS were identified using MIRPIPE

2021-05-24 | GSE69537 | GEO

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

Vineyard soil

Project description:Ion Torrent Sequencing_Soil Bacterial Metagenome

| PRJNA883056 | ENA

Project description:HBV RNA Ion Torrent sequencing

| PRJNA1015140 | ENA

Vineyard soil

Project description:Ion Torrent Sequencing_Soil Fungal Metagenome

| PRJNA885132 | ENA