Systematic evaluation of RNA-Seq preparation protocol performance
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PROVIDER: PRJNA543480 | ENA |
REPOSITORIES: ENA
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Project description:Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: TruSeq)
| PRJNA543482 | ENA
Project description:Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: SMARTer)
| PRJNA543483 | ENA
Project description:In this study, we present a comprehensive evaluation of four RNA-Seq library preparation methods. We used three standard input protocols, the Illumina TruSeq Stranded Total RNA and TruSeq Stranded mRNA kits, and a modified NuGEN Ovation v2 kit; and an ultra-low-input RNA protocol, the TaKaRa SMARTer Ultra Low RNA Kit v3. Our evaluation of these kits included quality control measures such as overall reproducibility, 5’ and 3’ end-bias, and the identification of DEGs, lncRNAs, and alternatively spliced transcripts. Overall, we found that the two Illumina kits were most similar in terms of recovering DEGs, and the Illumina, modified NuGEN, and TaKaRa kits allowed identification of a similar set of DEGs. However, we also discovered that the Illumina, NuGEN and TaKaRa kits each enriched for different sets of genes.
2019-06-27 | GSE131397 | GEO
Project description:In this study, we present a comprehensive evaluation of four RNA-Seq library preparation methods. We used three standard input protocols, the Illumina TruSeq Stranded Total RNA and TruSeq Stranded mRNA kits, and a modified NuGEN Ovation v2 kit; and an ultra-low-input RNA protocol, the TaKaRa SMARTer Ultra Low RNA Kit v3. Our evaluation of these kits included quality control measures such as overall reproducibility, 5’ and 3’ end-bias, and the identification of DEGs, lncRNAs, and alternatively spliced transcripts. Overall, we found that the two Illumina kits were most similar in terms of recovering DEGs, and the Illumina, modified NuGEN, and TaKaRa kits allowed identification of a similar set of DEGs. However, we also discovered that the Illumina, NuGEN and TaKaRa kits each enriched for different sets of genes.
2019-06-27 | GSE131396 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-06-27 | GSE131398 | GEO
Project description:The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and spike-ins comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. This SuperSeries is composed of the following subset Series: GSE9732: Spike-in Experiment for ChIP-chip Simulation GSE9842: Systematic evaluation of variability in simulated ChIP-chip experiments GSE9848: Systematic evaluation of variability in simulated ChIP-chip experiments Kevin_Encode GSE9849: Systematic evaluation of variability in simulated ChIP-chip experiments Myles_Encode GSE10004: ENCODE Spike-In, Yale Group GSE10076: ENCODE spikein, amplified DNA samples, NimbleGen arrays GSE10090: ENCODE spikein, nonamplified DNA samples, NimbleGen arrays GSE10112: Systematic evaluation of variability in simulated ChIP-chip experiments Keywords: SuperSeries For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series
2010-09-30 | E-GEOD-10114 | biostudies-arrayexpress
Project description:We report performance of six different protocols for small RNAseq library preparation and of a method utilizing sequencing of probes targeting microRNAs (HTG EdgeSeq). Recently, small RNA sequencing (small RNA-seq) has been introduced as a method for quantifying circulating microRNAs (miRNAs) and enabling their global profiling without prior knowledge of target sequences. Despite its great promise, small RNA-seq has not delivered the expected outcomes, particularly due to ligation and PCR bias introduced within the workflow. In this study, we assessed the performance of all existing approaches to the small RNA-seq of miRNAs in plasma samples: original two adapter ligation approach; single adapter ligation with subsequent circularization; polyadenylation; use of randomized adapters; and use of unique molecular identifiers (UMI). Using comprehensive set of metrics, we evaluated each protocol in terms of yield, precision, accuracy, sensitivity, and ability to detect isomiRs. Moreover, we assessed performance of targeted RNA-seq method utilizing hybridization probes across relevant metrics and together with RT-qPCR we used it as a reference for accuracy evaluation. The best results were delivered by targeted RNA-seq outperforming other methods in all relevant parameters. The protocols using randomized adapters or UMIs showed consistent good performance across all of the assessed metrics. In contrast, the polyadenylation approach generated a high percentage of discarded reads and impeded the analysis of isomiRs. The single adapter ligation with subsequent circularization failed to prevent ligation bias and the traditional two adapter ligation approach achieved the worse scores in the majority of tested metrics. To sum, we provide a comprehensive comparison that can serve as a guide for new users interested in analysis of circulating miRNAs and as a reference for further comparative studies.
2020-12-31 | GSE149513 | GEO
Project description:We systematically evaluated alternate strategies for WGBS studies, taking into account opportunites around library preparation methods, sequencing platforms and analysis pipeline optimization. We also assessed the performance and precision of the WGBS method relative to the methylation arrays, in an effort to provide data-driven recommendations for future WGBS studies, in particularly with respect to minimum coverage.
2019-07-29 | GSE128733 | GEO
Project description:We systematically evaluated alternate strategies for WGBS studies, taking into account opportunites around library preparation methods, sequencing platforms and analysis pipeline optimization. We also assessed the performance and precision of the WGBS method relative to the methylation arrays, in an effort to provide data-driven recommendations for future WGBS studies, in particularly with respect to minimum coverage.
2019-07-29 | GSE128731 | GEO
Project description:Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing
| PRJNA528654 | ENA