Project description:As part of a larger conifer genomics project, we developed a new 21.8K cDNA microarray containing 21,843 spotted ESTs from spruce (Picea spp.). To evaluate the performance of the array we conducted four technical replicate self-self hybridizations using untreated control bark RNA pooled from four biological replicates. The objectives were to determine: 1) the linear dynamic range of expression detection of the array; 2) the level of non-specific hybridization to negative control elements on the array; and 3) the overall technical reproducibility of the array. Keywords: Array performance evaluation using self-self hybridizations.
Project description:Reproducibility assessment is essential in extracting reliable scientific insights from high-throughput experiments. Inconsistency between technical replicates poses a challenge, particularly evident in NGS technologies based on immunoprecipitations, where the need for reproducibility in peak identification is a well-acknowledged limitation. While the Irreproducibility Discovery Rate (IDR) method has been instrumental in assessing reproducibility, its standard implementation is constrained to handling only two replicates. In the current era of steadly growing sample sizes, facilitated by multiplexing and reduced sequencing costs, highly performing methods that handle any number of replicates are desirable.
Project description:Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) datasets of three eHHV-6B-positive SLE patients (three technical replicates), six eHHV-6B-negative SLE patients (three technical replicates), and a negative control lacking sera or plasma (12 technical replicates; Illumina NextSeq) and sequencing data of HHV-6 peptide phage library (two technical replicates; Illumina NextSeq).
Project description:Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) datasets of three eHHV-6B-positive SLE patients (three technical replicates), six eHHV-6B-negative SLE patients (three technical replicates), and a negative control lacking sera or plasma (12 technical replicates; Illumina NextSeq) and sequencing data of HHV-6 peptide phage library (two technical replicates; Illumina NextSeq).
Project description:Cotton ovule development, mutant vs wild type, Comparisons of DP16 0 dpa ovule Keywords: WildType vs Mutant 7 comparisons and one 0 dpa control. The 1A/DP16 & 4A/DP16 comparisons have 8 slides each, 4 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The SL1-7-1/DP16 comparison has 6 slides, 3 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The 5B/DP16, fl/Xu-142, OI/II+N & 53/DP16 comparisons have 4 slides each, 2 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The 0 dpa control experiment has 3 slides , 3 Biological replicates, no technical replicates and no dye swapping.