Project description:RNA from in vitro grown Salmonella typhimurium is compared with RNA extracted from Salmonella typhimurium from infected chick caecums using a common DNA reference. Keywords: Disease state analysis, infected versus uninfected, common reference
Project description:RNA sequencing (RNA-seq) has been a widely used high-throughput method to characterize transcriptomic dynamics spatiotemporally. However, typical RNA-seq data analysis pipelines depend on either a sequenced genome or reference transcripts. This constriction makes the use of RNA-seq for species lacking both of sequenced genomes and reference transcripts challenging. To solve this problem, we developed CRSP, an RNA-seq pipeline integrating multiple comparative species strategy but not depending on a specific sequenced genome or reference transcripts. Benchmarking suggests the CRSP tool can achieve high accuracy to quantify gene expression levels.
Project description:we deep-sequenced two small RNA libraries made from V. longisporum infected/non-infected roots and employed Brassica rapa and Brassica oleracea genomes as reference for miRNA prediction and characterization as well. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to AA and CC genomes, respectively. Among them, 62 miRNAs were responsive to the V. longisporum infection.
Project description:RNA from in vitro grown Salmonella typhimurium is compared with RNA extracted from Salmonella typhimurium from infected chick caecums using a common DNA reference. Keywords: Disease state analysis, infected versus uninfected, common reference Five replicates from infected chick caecal contents compared to a common reference. Three replicates from in vitro grown Salmonella compared to a common reference. The common reference was genomic DNA and always occupies the Cy3 channel (channel 2).
Project description:Genomes of microorganisms that have been isolated in and on the human body, to be used as Reference Genomes for the Human Microbiome Project (HMP)
Project description:Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate annotation is of paramount importance. However, increasing evidence suggests annotated bacterial genomes have missed many, if not all, small genes encoding proteins ≤60 amino acids. To uncover unannotated small genes in Salmonella enterica, we used a genomic technique ‘ribosome profiling’ that provides a snapshot of all mRNAs being translated (translatome). For comprehensive identification of the small genes, we obtained Salmonella translatomes in four different growth conditions including Luria-Bertani medium, MOPS rich defined medium, N-minimal medium with low Mg2+ (10 μM), and N-minimal medium at pH 5.7, respectively. Ribosome profiling data were analysed in combination with in silico predicted putative open reading frames and transcriptome profiles. As a result, we uncovered 127 previously unannotated genes, the majority of which were small genes encoding proteins ≤50 amino acids. We validated expression by western blot of the identified unannotated small genes, the smallest of which is 7-amino acid long. Because some unannotated small genes identified in this study are only expressed in the infection-relevant low Mg2+ conditions, they are likely involved in cellular processes required for Salmonella virulence. Our findings suggest that currently sequenced bacterial genomes are likely under-annotated with regard to small genes and need to be revised.
