Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR244145_1.fastq.gz | Fastqsanger.gz | |||
| ERR244145_2.fastq.gz | Fastqsanger.gz | |||
| ERR244146_1.fastq.gz | Fastqsanger.gz | |||
| ERR244146_2.fastq.gz | Fastqsanger.gz | |||
| ERR244147_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 226 |
Similar Datasets
Project description:Aim: We aim to compare current (MeDIP-seq), new (Illumina Infinium 450K BeadChip) and future (PacBio) methods for whole genome DNA methylation analysis. As the interest in determination of disease methylation profiles increases, the scope, advantages and limitations of these methods requires assessment. There are key questions to answer and specific challenges to overcome. For example, how much detail/resolution is sufficient to identify regions of differential methylation and regions of biological/medical significance within a sample? How much coverage of the genome is required for accurate methylation analysis? Is it important to confirm which regions of the genome are unmethylated in addition to focusing on those that are methylated? Loss of methylation may be of equal importance within the cell since this may also contribute to disease pathogenesis. A multi-method (affinity enrichment/bisulphite-conversion based/direct sequencing of methyl-cytosine) and technology platform (Illumina HiSeq/PacBio/Illumina Infinium BeadChip) comparison will enable us to determine the strengths and weakness of each method. We propose to compare four methods using two DNA samples from the Coriell Institute for Cell Repository to assess both current and future capabilities for whole genome methylation analysis in parallel: A) MeDIP-seq using Illumina HiSeq B) Illumina Infinium HumanMethylation 450K BeadChip and C) whole genome methylation sequencing using PacBio. Existing single molecule deep bisulphite sequencing data generated previously from these same samples at the WTSI for targeted regions (30-40 genes) on the human X chromosome will be used to assess performance of each method. The methods selected for this study will generate data covering a range of resolutions from a whole genome scan to array (target defined) resolution and up to single base pair, single molecule resolution; the highest level of detail possible with methods currently available.Samples: DNA from sibling pair GM01240 (female) and GM01240 (male).Requirements: Both samples will be analysed using;A.MeDIP-seq using Illumina HiSeq (one HiSeq lane, 75bp paired end, per sample) B.Illumina Infinium HumanMethylation 450K BeadChipWe are expecting a potentially unnecessary high coverage using one HiSeq lane per sample. However, for the MeDIP procedure we do not have a multiplexing procedure in place. Our requirements for PacBio sequencing have been discussed with and will be supported by the Sequencing Technology Development group.
2013-01-22 | E-ERAD-139 | biostudies-arrayexpress
Project description:The LRGASP challenge encompasses different human, mouse, and manatee samples sequenced using multiple combinations of protocols and platforms. Different challenges will use distinct subsets of the samples for evaluation. The long-read sequencing platforms used in these challenges are the Pacific Biosciences (PacBio) Sequel II, Oxford Nanopore (ONT) MinION and PromethION. Samples will also be sequenced on the Illumina HiSeq 2500. The primary LRGASP library prep protocols are “standard” cDNA sequencing, direct RNA sequencing, R2C2, and CapTrap. Each sample will also include Lexogen SIRV-Set 4 spike-ins. We will also provide simulated PacBio and ONT data as part of the evaluations. This particular study focuses on single strand CAGE sequencing of human iPSCs, defining CAGE peaks from Illumina HiSeq 2500 (SR: 150 cycles) of two biological replicates for use in the LRGASP challenge.
2021-10-27 | GSE185917 | GEO
Project description:Next-generation sequencing for patient CH0219 using 454 and Illumina platforms
| PRJNA300287 | ENA
Project description:C.elegans small RNAs from HA::ALG-1, HA::ALG-2 and HA::RDE-1 IP and rde-1 mutants Small RNAs were cloned from transgenic or mutant C. elegans adults. Sequencing was performed using 454 and Illumina platforms.
2010-04-14 | E-GEOD-20649 | biostudies-arrayexpress
Project description:The methylation landscape of the cattle Y-chromosome was characterized using methylated cytosine data produced from PacBio and ONT long reads sequencing platforms.
2024-10-02 | GSE263098 | GEO
Project description:Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libraries from a biological sample as well as an equimolar pool of synthetic miRNAs and analyzed the results using capillary dideoxy sequencing and next-generation sequencing platforms (Roche/454, AB/SOLiD and Illumina/Solexa). Whereas different sequencing platforms provided highly similar results, large differences in DGE profiles were observed depending on the library preparation method used. Nevertheless, our results indicate that the preferential nature of the library preparation methods is systematic and highly reproducible and we show that DGE is well suited for the quantification of relative expression differences between samples. This SuperSeries is composed of the following subset Series: GSE16369: Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (454) GSE16370: Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (SOLiD) GSE16371: Limitations and possibilities of small RNA digital gene expression profiling: spleen and liver comparison (SOLiD) GSE16372: Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNAs replicates (SOLiD) GSE16373: Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNA replicates (Illumina) Refer to individual Series
2009-07-28 | E-GEOD-16374 | biostudies-arrayexpress
Project description:Comparing PacBio and Illumina platforms for fungal metabarcoding
| PRJNA414269 | ENA
Project description:The goal of this study was to use NGS RNAseq deep-sequencing in order to characterize the complement of polyadenylated mRNAs and lncRNAs expressed in LNCaP, a prostate cancer cell line. RNA-seq data were processed as aggregates of the two biological replicates to increase resulting transcriptome coverage. Trimmed reads were mapped with TopHat v.2.0.12 and Bowtie v.2.2.3, and a custom GTF file to guide transcriptome assembly. This custom GTF file was built by using the human transcriptome annotation GTF file downloaded from Ensembl Project web-site (http://www.ensembl.org/) and modified to include all lncRNAs reported in Cabili et al, Genes & Development 2011. polyA+ RNA profiles of LNCaP prostate cancer cell line grown in culture for 48 h in the absence of androgen were generated by paired-end deep sequencing, in duplicate, using Illumina HiSeq2000.
2016-09-08 | E-GEOD-79301 | biostudies-arrayexpress
Project description:The methylation landscape of the sheep Y-chromosome was characterized using methylated cytosine data produced from PacBio and ONT long reads sequencing platforms. The study aimed to corroborate the presumptive locus of the sheep Y-chromosome centromere.
2024-10-02 | GSE262831 | GEO