Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dd2c5785-73b6-47ea-b3b5-435fffb96d10 - samples

ABSTRACT: The dataset contains three BAM files that include SPATC1L variants identified in Italian patients affected by hearing loss (both hereditary and age-related hearing loss). Data have been produced by whole exome sequencing and targeted re-sequencing, using Ion Proton and Ion Torrent PGM platforms respectively.

PROVIDER: EGAD00001004147 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

c8655079-ad38-4708-a0f1-baf41656b4ed - samples

Project description:The dataset contains one BAM file that includes a SLC9A3R1 variant identified in two Italian patients affected by age-related hearing loss. Data have been produced by targeted re-sequencing, using Ion Torrent PGM platform.

| EGAD00001004171 | EGA

Expression analysis after PNLDC1 silencing in E14 cells

Project description:Next generation sequencing using the Ion Torrent PGM platform after PNLDC1 silencing in mouse embryonic stem cells E14 using esiRNA

2016-09-12 | GSE83405 | GEO

MicroRNA sequencing of mouse soleus muscle

Project description:MicroRNA sequencing using Ion Torrent Proton platform

2015-03-31 | GSE63342 | GEO

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

Project description:Ion Torrent PGM sequencing for microbial ecology

| PRJEB7667 | ENA

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

Project description:Background: Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case. Results: Here we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features; for example, disentangling the source of expression in gene-pseudogene pairs. Conclusions: Taken together, our results indicate that while Illumina and Ion Torrent have similar capacities to detect changes in biology from a treatment/control experiment, these platforms may be tailored to interrogate different transcriptional phenomena through careful selection of alignment software.

2017-08-04 | GSE98562 | GEO

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

MicroRNA sequencing of mouse soleus muscle

Project description:MicroRNA sequencing using Ion Torrent Proton platform Single run of a pool of m.soleus from 5 male mice

2015-03-31 | E-GEOD-63342 | biostudies-arrayexpress

RNA-Seq of hematopoietic stem cells from vehicle and estrogen-treated mice

Project description:Purpose: The goals of this study were to determine genes in HSCs that are regulated by estrogen. Methods: mRNA profiles of vehicle and estrogen treated wild-type (WT) and Esr1fl/fl;Mx1-Cre (ERa-KO) HSCs were generated by deep sequencing using Illumina HiSeq 2000 and Ion Torrent Proton platforms. The sequence reads that passed quality filters were analyzed at the transcript isoform level using DE-Seq2. qRT–PCR validation was performed using SYBR Green assays

2017-10-01 | GSE99120 | GEO

SPATC1L variants associated with age-related and hereditary hearing loss

Project description:Next-Generation Sequencing techniques (i.e, targeted re-sequencing and whole exome sequencing) have been employed for the study of two Italian patients affected by age-related hearing loss and of an Italian family affected by hereditary hearing loss. Data analysis led to the identification of three variants in SPATC1L, associated with the clinical phenotype.

| EGAS00001003047 | EGA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data