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.
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.
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes
Project description:The most widely-used method for detecting and measuring genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Many tiling array platforms, amplification methods, and analysis algorithms exist for ChIP-chip, but a rigorous assessment of the relative performance of these factors has not been reported. In a multi-lab simulation of a ChIP-chip experiment, we conducted the first objective analysis of tiling array platforms and analysis algorithms. We designed a complex mixture of human genomic DNA with a "spike-in" comprised of nearly 100 human sequences at various concentrations. Eight independent groups hybridized these mixtures to four different tiling array platforms. The groups were blind to the composition of the spike-in mix, the range of concentrations covered, or how many sequences it contained. Still blind to the key, each group made predictions of the spike-in locations based on their measurements. The results reveal that all commercial tiling array platforms perform well, although each platform and analysis algorithm has distinct performance characteristics. Simple sequence repeats and genome redundancy tend to result in false positives on oligonucleotide platforms. We also compare genome-wide platforms with regard to performance and cost. The spike-in DNA samples and the resulting array data presented in our study provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. Keywords: Spike in Control For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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 and analysis 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. All commercial tiling array platforms performed well, although each platform and analysis algorithm had distinct performance and cost characteristics. Simple sequence repeats and genome redundancy tend to result in false positives on oligonucleotide platforms. The spike-in DNA samples and the resulting array data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. Keywords: chip-ChIP simulation For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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
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.