Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A transcriptome map of Actinobacillus pleuropneumoniae at single-nucleotide resolution using RNA-seq

ABSTRACT: We used the RNA-seq technology to do a genome-wide transcriptional analysis of A. pleuropneumoniae strain JL03 and investigated the transcriptome structure at a single-nucleotide resolution.The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures). Transcript profiling of a single sample by RNA-Seq

ORGANISM(S): Actinobacillus pleuropneumoniae serovar 3 str. JL03

SUBMITTER: Lu Li

PROVIDER: E-GEOD-70153 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genomeM-bM-^@M-^Ys primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide, nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally-engaged RNA polymerases in mouse embryonic stem cells (ESCs) and embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ~40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol IIM-bM-^@M-^Ys entry into elongation. Furthermore, M-bM-^@M-^\bivalentM-bM-^@M-^] ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb Group Complexes PRC 1 and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5M-bM-^@M-^Y proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation. Mapping engaged RNA polymerase density in two cell types by sequencing run-on transcripts. SUPPLEMENTARY FILES: All fastq files have sanger-fastq format q values. Alignments were generated with eland and the mm9 mouse genome assembly. Reads aligning to regions annotated as similar to rRNA by RepeatMasker were then removed. Wiggle files are in units of RPKM (reads per kilobase per million aligned reads) and are broken up by cell type and chromosome to aid in uploading to UCSC. Each file furthermore contains two tracks - one for each strand. As in the published paper, plus strand RPKM densities are in red with positive values and minus strand RPKM densities are in blue with negative values.

Project description:Using Solexa/Illumina's digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated the kinetic transcriptional profile of gene expression in macrophages infected with Brucella melitensis strain 16M. A key aspect of Brucella virulence is their ability to proliferate within professional and nonprofessional phagocytic host cells, thereby successfully bypassing the bactericidal effects of phagocytes. Their virulence and chronic infections are thought to be due to their ability to avoid the killing mechanisms within host cells. Defining the interaction between a host cell and Brucella is crucial to understanding the infectious process. Most researchers have studied the pathogens, but the host plays a very important role during infections. To date, relatively few host factors have been shown important in Brucella infections. However, little is known about the host networks that mediate infection. The objective of the study is to analyze the genes and cellular components related to the innate immunity response to determine the mechanisms through which Brucella avoids the host innate immunity. A total of 3576 and 3962 genes that are differentially expressed between 0 and 4 h and between 0 and 24 h were identified. The identified genes are related to immune processes, signal transduction, inflammation, apoptosis, cell membrane, transcriptional regulation, and intracellular trafficking. Our data have added to the current understanding of different host gene expressions during different infection phases by Brucella spp. The RAW264.7 cells were seeded into 24-well plates at 5-105 cells/well, incubated in 5% CO2 at 37 M-BM-0C for 24 h, and then infected with Brucella at a multiplicity of infection of 200. To synchronize the infection, the infected plates were centrifuged at 200 ug for 5 min at room temperature and then incubated at 37 M-BM-0C for 20 minutes. The infected cell monolayers were washed three times with PBS, overlaid with 0.5 ml of DMEM containing 100 mg/ml of ampicillin and 50 mg/ml of kanamycin at 37 M-BM-0C for 0, 4, and 24 h. At the end of the incubation period, the culture medium was removed and centrifuged at 1500 rpm for 15 min. The cell pellet and adherent cells were resuspended in TRIzol. Total RNA were extracted from the cells at 0, 4 and 24 h post infection.

Dataset Information

A transcriptome map of Actinobacillus pleuropneumoniae at single-nucleotide resolution using RNA-seq

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets