Ontology highlight
ABSTRACT:
PROVIDER: PRJNA863749 | ENA |
REPOSITORIES: ENA
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Project description:We infected wild type L. monocytogenes EGD-e (1) and its isogenic deltahlydeltaplcA (2) (lacking the ability to breach the vacuolar compartment of host cells following uptake) mutant strain to human intestinal epithelial cell line (Caco-2) with an MOI of 100 and 500 respectively. Bacterial total RNA was isolated at 1 h (deltahlydeltaplcA) and 4 h (EGD-e) post infection, reverse transcribed, hybridised to whole genome microarray and microarray data was analysed as described previously (3) 1. Glaser et al. 2001. Comparative genomics of Listeria species. Science 294:849-852. 2. Paschen et al. 2000. Human dendritic cells infected by Listeria monocytogenes: induction of maturation, requirements for phagolysosomal escape and antigen presentation capacity. Eur.J.Immunol. 30:3447-3456. 3. Chatterjee et al. 2006. Intracellular gene expression profile of Listeria monocytogenes. Infect.Immun. 74:1323-1338.
2008-06-18 | E-MEXP-1144 | biostudies-arrayexpress
Project description:Using integrated genomics we identify a role for CLEC12A in antibacterial autophagy. Clec12a-/- mice are more susceptible to bacterial infection and CLEC12A deficient cells exhibit impaired antibacterial autophagy. We used transcriptional profilinf to understand the role of CLEC12A in the response to Salmonella and Listeria.
2015-06-30 | GSE69132 | GEO
Project description:Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site (TSS) maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. Our data revealed conservation across most transcripts, but significant divergence between the species in a subset of non-coding RNAs. In L. monocytogenes we identified 113 sRNAs and 70 asRNAs, significantly increasing the repertoire of non coding RNAs in this species. Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 5M-bM-^@M-^Y UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such lasRNA/operon structure, termed "excludon", might represent a novel form of regulation in bacteria. Construction of consensus TSS-maps in Listeria monocytogenes and Listeria innocua by applying 5'-end sequencing on samples in different conditions and genetic backgrounds.
2012-05-01 | E-GEOD-36060 | biostudies-arrayexpress
Project description:Osteosarcomas (OS) have highly chaotic genomes, yet their cancer drivers are poorly defined. Given that cancer genes are conserved among mammals, cross-species genomics of naturally arising cancers opens a powerful approach to identifying oncogenic drivers to broaden the therapeutic opportunities for aggressive cancers. Here, we utilized a dog-to-human cross-species genomics combined with gain- and loss-of-function analysis to uncover novel OS driver genes.
2021-08-03 | GSE118130 | GEO
Project description:Ileal profiles from gnotobiotic mice mono-associated with Listeria species or B. thetaiotaomicron. Samples were derived from 72h colonizations of Fabpi-hEcad transgenic B6 mice fed a standard-chow polysaccharide rich (PR) diet. Keywords: Germ-free vs. Mono-associations
2007-04-23 | GSE7013 | GEO
Project description:Using integrated genomics we identify a role for CLEC12A in antibacterial autophagy. Clec12a-/- mice are more susceptible to bacterial infection and CLEC12A deficient cells exhibit impaired antibacterial autophagy. We used transcriptional profilinf to understand the role of CLEC12A in the response to Salmonella and Listeria. Bone marrow-derived macrophages from WT or Clec12a-/- mice were infected with Salmonella enterica serovar Typhimurium or Listeria monocytogenes. Cells were harvested at 0,3,6, and 24hours post-infection for RNA analysis. Please note that single-end sequencing was performed but two files: R1 files that contained the sample barcodes (19 or 17bp reads) and R2 files that contained the single-end-sequenced 46bp cDNA reads were generated. Since the barcode info is mostly redundant, only R2 reads were submitted (described in 'raw_file_readme.txt').
2015-06-30 | E-GEOD-69132 | biostudies-arrayexpress
Project description:Genomics and Transcriptomics of Listeria monocytogenes
| PRJNA1112861 | ENA
Project description:Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment.
2017-11-20 | GSE98013 | GEO
Project description:In several gram-positive bacterial genera including Bacillus, Staphylococcus, and Listeria, sigma B (σB) has been identified as a stress-responsive alternative sigma factor responsible for initiating transcription of genes (the σB regulon) involved in response to stress-inducing environmental conditions. In L. monocytogenes, a foodborne pathogen of considerable threat to public health and the food industry, σB is involved in regulation of stress response and virulence gene expression. We have defined the σB regulon in L. monocytogenes during early stationary phase and under salt stress (0.3M NaCl) conditions using whole-genome microarrays, identifying 168 genes that generated ≥2.0-fold higher signals in the parental strain 10403S than in an isogenic sigB null mutant (ΔsigB), categorized into nine functional groups including stress-response genes (12), virulence genes (5), and genes related to transport (26) and metabolism (45). To gain a broader biological perspective of the σB stress response system, we applied these microarrays to Listeria innocua under the same environmental conditions. Our studies revealed 64 candidates in the L. innocua σB regulon with ≥2.0-fold higher signals in the parent than in a ΔsigB mutant; 49 of the 64 genes overlap with the L. monocytogenes σB regulon, indicating extensive overlap in σB-controlled genes between the two species. Further transcriptional analysis using TaqMan quantitative real time RT-PCR was performed for selected genes that displayed contrasting fold changes among the four microarray data sets (two stress conditions per species). We report novel members of the L. monocytogenes σB regulon, as well as the initial definition of the L. innocua σB regulon. Our comparative studies of the σB stress response systems in L. monocytogenes and L. innocua revealed features of the σB regulon that are conserved and unique to the two species. Keywords: Listeria monocytogenes, Listeria innocua, SigB regulon, salt stress, stationary phase
2007-11-29 | GSE7492 | GEO