Project description:Raw data of TMT-labeled proteome of Chinese breast cancers. Uploaded by Zhi-Ming Shao Lab, Fudan University Shanghai Cancer Center (FUSCC)
Project description:To study their metabolic potential in natural ecosystems, we developed a species-independent LAB microarray, containing 2,269 30-mer oligonucleotides, and targeting 406 genes that play a key role in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response. Also, genes linked to negative traits such as antibiotic resistance and virulence are represented. This experiment is a validation experiment, where we hybridized labelled DNA from 20 LAB strains, covering 86% of all oligos. Keywords: Platform validation experiment
Project description:Based on the different chemistries of phenol extraction of RNA versus commercial kits, we hypothesized that certain species of mRNA may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq experiments. We tested this using Saccharomyces cerevisiae samples that only differ in the RNA isolation method: a "standard" hot phenol extraction, versus two different commercial RNA isolation kits. While the kits had comparable relative mRNA abundances, samples isolated with hot phenol had higher relative abundance of mRNAs encoding membrane proteins. We hypothesize that hot phenol better solubilizes mRNAs associated with cellular membranes. We then compared the effects of each RNA isolation method on the ability to identify differentially expressed transcripts, using the yeast heat shock response a test case. The method of RNA isolation had little effect on the ability to identify differentially expressed transcripts. Thus, experiments within a single lab are unlikely to be affected by the choice of RNA isolation method as long as the same method is used throughout an experiment. For meta-analyses however, researchers should be cautious if trying to compare experiments where the RNA isolation methods differ.
Project description:A consortium of ten labs from the DC and Baltimore area was formed to compare three leading platforms. Each lab was given identical RNA samples (A1 and B1) which were processed according to what each lab considered best practice. Five of the labs used Affymetrix GeneChips, three used two-color spotted cDNA arrays, and two used two-color long oligo arrays. Keywords: repeat sample
