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ABSTRACT:
PROVIDER: PRJNA858941 | ENA |
REPOSITORIES: ENA
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Project description:This is a companion study to (GSE21342). Peripheral blood leukocyte samples were obtained with consent from 100 red cross blood donors sampled cross-sectionally across the city of Brisbane, Australia. After correction for RNA integrity values, individuals fall into major profiles of expression variation suggesting environmental and cultural influences on immune gene expression. 100 individuals, 50 men and 50 women, were sampled with permission of the Red Cross Society of Australia and under informed consent. The age of individulas were between 18 and 68 (mean 44). BMI ranged from 17.7 to 51.3 with a mean of 26.6. Collection was carried out by EM at mobile Red Cross vans at 10 locations (Bellbowrie, Capalaba, Dayboro, Eagle Farm, Kenmore, Mount Ommaney, South Brisbane, St Lucia, Virginia, and Woolloongabba) distributed across the city.
2011-01-01 | E-GEOD-21311 | biostudies-arrayexpress
Project description:This study was to compare gene expression profiles of human AMLs that either carry or lack potentially deleterious variants in genes of the Fanconi Anemia-Homologous Recombination DNA repair network” . Variants were identified by whole exome sequencing of the relevant genes. In total, 145 AML Diagnosis Samples were arrayed with no duplicates. CD34+ cells were used as normal controls. CML and normal Mono-nuclear cells (MNC) samples were not used for analysis. Adelaide Samples were sourced from the South Australian Cancer Research Biobank, ALLG Samples were sourced from the Australian Leukaemia an Lymphoma Group
2015-07-14 | E-GEOD-67936 | biostudies-arrayexpress
Project description:We used our newly ultra deep sequence data and bioinformatics to re-annotate P. xylostella genome for high confidence miRNAs with the correct 5p and 3p arm features. Furthermore, the whole genome was screened to identify potential miRNA binding sites using three target-predicting algorithms. Totally, 203 mature miRNAs were annotated, including 33 novel miRNAs. Two geographical populations of Diamondback moth larvae from Queensland (Gatton) and South Australia (Waite) were collected and reared on the cabbage plant at the University of Queensland in Australia. Total RNA was extracted from fifteen 3rd instar larval samples using Triazol® following the manufacturerâs protocol (Life Technologies). The small RNA libraries were generated from both populations with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illuminaâs Sequencing Control Studio software.
2016-08-01 | E-GEOD-76321 | biostudies-arrayexpress
Project description:Companion Animal Food Metagenome
| PRJNA1062328 | ENA
Project description:specific pathogen-free female BALB/c mice aged 7-8 weeks (Animal Resources Centre, Perth, Western Australia) were systemically sensitised by intraperitoneal injection of 50 M-5g of alum-precipitated chicken egg OVA (Grade V, ?98% pure, Sigma Australia) 21 and 7 days before inhalational challenge, then exposed to aerosolised OVA in a whole body inhalation exposure chamber (Unifab Corporation, Kalamazoo, MI). Chronic low-level challenge involved exposure to ?3 mg/m3 aerosolised OVA for 30 minutes/day on 3 days/week for up to 6 weeks. Particle concentration within the chamber was continuously monitored using a DustTrak 8520 instrument (TSI, St Paul, MN). All experimental procedures complied with the requirements of the Animal Care and Ethics Committee of the University of New South Wales (reference numbers: 06/119B and 08/09B). Mice were sacrificed after 1,2,4 and 6 weeks of OVA exposure. Control groups included naM-ove mice and mice that were not sensitised but were challenged for 6 weeks with aerosolised OVA.
2011-06-10 | E-MEXP-3118 | biostudies-arrayexpress
Project description:This is a companion study to (GSE21342). Peripheral blood leukocyte samples were obtained with consent from 100 red cross blood donors sampled cross-sectionally across the city of Brisbane, Australia. After correction for RNA integrity values, individuals fall into major profiles of expression variation suggesting environmental and cultural influences on immune gene expression.
2011-01-01 | GSE21311 | GEO
Project description:A collection of 61 Salmonella enterica serovar Typhimurium (S. Typhimurium) of animal and human origin, matched as closely as possible by phage type, antimicrobial resistance pattern and place / time of isolation, and sourced from farms or hospitals in Scotland, were analysed by antimicrobial susceptibility testing, phage typing, pulsed field gel electrophoresis (PFGE), plasmid profiling and DNA microarrays. PFGE of all 61 isolates revealed ten PFGE profiles, which clustered by phage type and antibiotic resistance pattern, with human and animal isolates distributed between PFGE profiles. Analysis of 23 representative S. Typhimurium strains hybridised to a composite Salmonella DNA microarray identified a small number of specific regions of genome variation between different phage types and PFGE profiles. These variable regions of DNA were typically located within prophage-like elements. Simple PCR assays were subsequently designed to discriminate between different isolates from the same geographical region.
2007-06-09 | E-SGRP-6 | biostudies-arrayexpress
Project description:Genome-wide MeDIP-Sequencing of 23 monozygotic twin pairs (n=46) from Australia discordant for major depressive disorder (MDD).
2014-01-25 | GSE54370 | GEO
Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-Barré and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. Keywords: comparative genomic indexing analysis
2007-12-19 | GSE9862 | GEO