GNPS - Ascaroside Alkyne Labeling and Metabolism
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Caenorhabditis Elegans (ncbitaxon:6239)
SUBMITTER: 
Frank Schroeder
PROVIDER: MSV000086092 | GNPS |
REPOSITORIES: GNPS
Similar Datasets
Project description:Metabolic labeling of Hek293 cells using 4-thiouracil
| PRJNA476121 | ENA
Project description:Tracking chromatin state changes using nanoscale protoproximity labeling
| PRJNA915358 | ENA
Project description:Off-the-shelf proximity labeling
| PRJNA716256 | ENA
Project description:Tracking chromatin state changes using nanoscale protoproximity labeling (RNA-Seq)
| PRJNA915472 | ENA
Project description:Tracking chromatin state changes using nanoscale protoproximity labeling (ATAC-Seq)
| PRJNA915471 | ENA
Project description:Considerable variation in gene expression data from different DNA microarray platforms has been demonstrated. However, no characterization of the source of variation arising from labeling protocols has been performed. To analyze the variation associated with T7-based RNA amplification/labeling methods, aliquots of the Stratagene Human Universal Reference RNA were labeled using 3 eukaryotic target preparation methods and hybridized to a single array type (Affymetrix U95Av2). Variability was measured in yield and size distribution of labeled products, as well as in the gene expression results. All methods showed a shift in cRNA size distribution, when compared to un-amplified mRNA, with a significant increase in short transcripts for methods with long IVT reactions. Intra-method reproducibility showed correlation coefficients >0.99, while inter-method comparisons showed coefficients ranging from 0.94 to 0.98 and a nearly two-fold increase in coefficient of variation. Fold amplification for each method was positively correlated with the number of present genes. Two factors that introduced significant bias in gene expression data were observed: a) number of labeled nucleotides that introduces sequence dependent bias, and b) the length of the IVT reaction that introduces a transcript size dependent bias. This study provides evidence of amplification method dependent biases in gene expression data. Keywords: method validation study
2006-01-01 | GSE3254 | GEO
Project description:To characterize the properties and evaluate the performance of the TAcKLE procedure, a novel method providing effective transcriptome amplification for expression analyses on oligonucleotide microarrays, we performed 20 two-color hybridizations using self-spotted Operon 27k arrays. A single source of universal human reference RNA (pooled from 10 cell lines) and RNA extracted from healthy breast tissue was used for all experiments to avoid differences in transcript abundance imposed by the RNA preparation. RNA was either amplified by one or two rounds of linear isothermal RNA amplification (starting from 2000 ng, 200 ng, 20 ng or 2 ng), followed by Cy-dUTP incorporation using Klenow fragment, or labeled directly by reverse transcription of 40 µg RNA with Cy-dUTP. For all quantities of starting material, one co-hybridization of reference RNA, two hybridizations of breast versus reference RNA as well as one hybridization of reference versus breast RNA were performed. In case of amplified RNA, all dye labeling reactions were made from distinct target preparations. Hybridizations were performed for 16 h at 42 °C in a GeneTAC Hybridization Station (Genomic Solutions) using UltraHyb hybridization buffer (Ambion). Hybridized microarrays were scanned at 5 µm resolution on a GenePix 4000B microarray scanner (Axon Instruments). For all hybridizations, raw signal intensities were normalized applying variance stabilization (W. Huber et al., Bioinformatics 18 Suppl 1, 2002). Keywords = amplification Keywords = labeling Keywords = protocol Keywords = spotted Keywords = human Keywords = long oligonucleotide Keywords = oligo Keywords = 70mer Keywords = Operon Keywords: other
2004-08-13 | GSE1645 | GEO
Project description:Interventions: Carbon nanoparticle suspension labeling group:None;Ordinary enteroscopy group:None
Primary outcome(s): Length of distal incisal margin;Excision length of intestine;Lymph node acquisition;Length of submucosal invasion
Study Design: Cohort study
| 85121 | ecrin-mdr-crc
Project description:Several technical parameters are now being optimized for microRNA expression profiling experiments, but the finite amount of total RNA available continues to bottleneck clinical investigations. We used microarrays to determine the influence of the labeling reagent on total RNA requirements and data quality. Human brain/lung samples were each labeled in duplicate, at 1.0ug, 0.5ug, 0.2ug, and 0.1ug of total RNA, using two microRNA labeling kits (Genisphere Biotin and Biotin-HSR) that utilize the same labeling procedure but differ in the composition of the labeling reagent used to label the microRNA molecules in the samples. A total of 32 arrays were used for this experiment. Additionally, synthetic microRNA spike-in experiments were also performed to establish the signal dynamic range of the microarray using the Biotin-HSR labeling kit. Two-fold serial dilution samples were prepared that contained from 5000 to 4.88 attomoles of miRNA. A total of 12 arrays were used for this experiment, including a negative control sample.
2012-05-21 | E-GEOD-30045 | biostudies-arrayexpress
Project description:Dynamic isotope labeling data provide crucial information about the operation of metabolic pathways, and are commonly generated via liquid chromatography mass spectrometry (LC-MS). Metabolome-wide analysis is challenging as it requires grouping of metabolite features over different samples. We developed DynaMet for fully automated investigations of isotope labeling experiments from LC-high resolution MS raw data. DynaMet enables untargeted extraction of metabolite labeling profiles and provides integrated tools for expressive data visualization. For this study we generated labeling data of the model strain Escherichia coli from 13C glucose labeling switch experiments. Analysis of two biological replicates revealed high robustness and reproducibility of the pipeline. DynaMet analysis of two data sets each comprising 19 samples resulted in 286 and 293 features, respectively, with detection in at least 80% of all samples analyzed. Of these, 222 and 230, respectively, could be fitted with the implemented model. After removing false positives and merging both data sets DynaMet revealed a total number of 291 features with labeling profiles whereof 285 could be generated with implemented fitting function. Comparison with KEGG database resulted in 125 matches corresponding to 98 metabolites covering multiple pathways of core metabolism and major biosynthetic routes. The study results reported here are only a summary. To reproduce the complete results i.e. labeling profiles and corresponding kinetic fits including plots, DynaMet software is required.
2015-10-19 | MTBLS229 | MetaboLights