Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Performance comparison and in-silico harmonisation of commercial platforms for DNA methylome analysis by targeted bisulfite sequencing

ABSTRACT: Performance comparison and in-silico harmonisation of commercial platforms for DNA methylome analysis by targeted bisulfite sequencing

PROVIDER: PRJEB46506 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	ERR6594540_1.fastq.gz	Fastqsanger.gz
	ERR6594540_2.fastq.gz	Fastqsanger.gz
	ERR6606780_1.fastq.gz	Fastqsanger.gz
	ERR6606780_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 129

Similar Datasets

Performance Evaluation of Commercial miRNA Expression Array Platforms

2010-03-18 | GSE19248 | GEO

Performance Evaluation of Commercial miRNA Expression Array Platforms

Project description:This data is part of a miRNA platform comparison study. We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance. The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision. Performance of four (4) commercially available miRNA platforms was evaluated using 7 placenta samples spiked with synthetic microRNA spikes (in Latin-square design) absent in placenta. Platforms were primarily evaluated for accuracy and specificity.

2010-06-23 | E-GEOD-19248 | biostudies-arrayexpress

Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue

Project description:This SuperSeries is composed of the following subset Series: GSE30120: Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue [NimbleGen] GSE30121: Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue [Agilent] Refer to individual Series

2012-01-17 | E-GEOD-30123 | biostudies-arrayexpress

Transcription profiling of human bone tumours to evaluate four commercial high-resolution oligonucleotide microarray platforms.

Project description:Evaluation of four commercial high-resolution oligonucleotide microarray platforms, Affymetrix Genome-Wide Human SNP Array 6.0, Agilent Human Genome CGH 244A, Illumina HumanExon510s-duo and Nimblegen HG18 CGH 385k WG tiling v1.0, for genomic profiling of bone tumours.

2010-07-01 | E-TABM-805 | biostudies-arrayexpress

Performance evaluation of commercial miRNA expression array platforms.

Project description:BackgroundmicroRNAs (miRNA) are short, endogenous transcripts that negatively regulate the expression of specific mRNA targets. The relative abundance of miRNAs is linked to function in vivo and miRNA expression patterns are potentially useful signatures for the development of diagnostic, prognostic and therapeutic biomarkers.FindingWe compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance.ConclusionsThe Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision.

| S-EPMC2853548 | biostudies-literature

Bisulfite methylome sequencing of msh1 memory line in arbidopsis [Bisulfite-seq]

Project description:MSH1 depletion caused whole genome wide Methylome changes in Arabidopsis, to conduct comparative genomic analysis, here we generate methylome for MSH1-RNAi line and transgene segregated out msh1 memory line

2018-06-01 | GSE106309 | GEO

Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues

Project description:Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of three well-established high throughput 3’-scRNAseq platforms: Drop-seq, 10x Chromium and BD Rhapsody; using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10x Chromium have similar but higher gene sensitivity than Drop-seq, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10x Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.

2024-09-04 | GSE229765 | GEO

Performance comparison of four commercial human whole-exome capture platforms.

Project description:Whole exome sequencing (WXS) is widely used to identify causative genetic mutations of diseases. However, not only have several commercial human exome capture platforms been developed, but substantial updates have been released in the past few years. We report a performance comparison for the latest release of four commercial platforms, Roche/NimbleGen's SeqCap EZ Human Exome Library v3.0, Illumina's Nextera Rapid Capture Exome (v1.2), Agilent's SureSelect XT Human All Exon v5 and Agilent's SureSelect QXT, using the same DNA samples. Agilent XT showed the highest target enrichment efficiency and the best SNV and short indel detection sensitivity in coding regions with the least amount of sequencing. Agilent QXT had slightly inferior target enrichment than Agilent XT. Illumina, with additional sequencing, detected SNVs and short indels at the same quality as Agilent XT, and showed the best performance in coverage of medically interesting mutations. NimbleGen detected more SNVs and indels in untranslated regions than the others. We also found that the platforms, which enzymatically fragment the genomic DNA (gDNA), detected more homozygous SNVs than those using sonicated gDNA. We believe that our analysis will help investigators when selecting a suitable exome capture platform for their particular research.

| S-EPMC4522667 | biostudies-literature

Bisulfite methylome sequencing of msh1 memory line in tomato

2018-06-30 | GSE105008 | GEO

Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue [Agilent]

Project description:Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH. Aim of the present study is to compare aCGH platforms suitable for copy number analysis using FFPE derived DNA. Two dual channel aCGH platforms (Agilent and NimbleGen) and a single channel SNP based platform (Affymetrix), were evaluated using seven FFPE colon cancer samples, median absolute deviation (MAD), deflection, signal-to-noise ratio (SNR) and DNA input requirements were used as quality criteria. Large differences were observed in MAD values and deflection between platforms; Agilent and NimbleGen showed better MAD values (0.13 for both) compared to Affymetrix (0.22). Contrary, Affymetrix showed a better deflection of 0.94, followed by 0.71 for Agilent and 0.51 for NimbleGen. Since the deflection compensates for the MAD the Signal to Noise Ratios (SNR) were comparable; Agilent ranks first, Affymetrix second and NimbleGen third with SNRs of 3.9, 3.6 and 3.3 respectively. DNA input amounts of 40ng are sufficient for high quality profiles with Affymetrix. For Agilent DNA input amounts of 50ng are sufficient for high quality profiles. For results of similar quality NimbleGen requires at least 100ng. Copy number analysis using DNA derived from FFPE archival material is feasible and shows reproducible results on high-resolution copy number platforms. Input amounts of DNA from FFPE material lower than recommended still yield high quality profiles without additional amplification steps.

2012-01-17 | GSE30121 | GEO

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