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Transcriptome of Arabidopsis APS kinase null mutants

ABSTRACT: The aim of the experiment is to look at transcriptional changes in null mutants of APS kinase. There are four APS kinase isoforms in Arabidopsis, we are interested in the double mutant APK1/APK2, created by crossing two single salk lines. The transcriptomes of WT (Col-0) plants and the double knockout (ab) will be compared. The plants were grown under controlled environment conditions of 10h day, 14h night, 22 degrees centigrade, 60% humidity for five weeks. 10 whole rosettes were pooled for each replicate, there are three replicates for each genotype. Keywords: Expression profilling by array

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE18980 | GEO | 2009/11/18

SECONDARY ACCESSION(S): PRJNA120969

REPOSITORIES: GEO

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Transcriptome of Arabidopsis APS kinase null mutants

Project description:The aim of the experiment is to look at transcriptional changes in null mutants of APS kinase. There are four APS kinase isoforms in Arabidopsis, we are interested in the double mutant APK1/APK2, created by crossing two single salk lines. The transcriptomes of WT (Col-0) plants and the double knockout (ab) will be compared. The plants were grown under controlled environment conditions of 10h day, 14h night, 22 degrees centigrade, 60% humidity for five weeks. 10 whole rosettes were pooled for each replicate, there are three replicates for each genotype. Keywords: Expression profiling by array 6 samples were used in this experiment

2009-11-17 | E-GEOD-18980 | biostudies-arrayexpress

Mus musculus APS

Project description:Mus musculus APS Raw sequence reads

| PRJNA849534 | ENA

The antimicrobial peptide-sensing system aps of Staphylococcus aureus

Project description:Staphylococcus aureus is a leading cause of hospital-associated infections. In addition, highly virulent strains of methicillin-resistant S. aureus (MRSA) are currently spreading outside health care settings. Survival in the human host is largely defined by the ability of S. aureus to resist mechanisms of innate host defense, of which antimicrobial peptides form a key part especially on epithelia and in neutrophil phagosomes. Here we demonstrate that the antimicrobial-peptide sensing system aps of the standard community-associated MRSA strain MW2 controls resistance to cationic antimicrobial peptides. The core of aps-controlled resistance mechanisms comprised the D-alanylation of teichoic acids (dlt operon), the incorporation of cationic lysyl-phosphatidylglycerol (L-PG) in the bacterial membrane (mprF), and the vraF/vraG putative antimicrobial peptide transporter. Further, the observed increased production of L-PG under the influence of cationic antimicrobial peptides was accompanied by the up-regulation of lysine biosynthesis. In noticeable difference to the aps system of S. epidermidis, only selected antimicrobial peptides strongly induced the aps response. Heterologous complementation with the S. epidermidis apsS gene indicated that this is likely caused by differences in the short extracellular loop of ApsS that interacts with the inducing antimicrobial peptide. Our study shows that the antimicrobial peptide sensor system aps is functional in the important human pathogen S. aureus, significant interspecies differences exist in the induction of the aps gene regulatory response, and aps inducibility is clearly distinguishable from effectiveness towards a given antimicrobial peptide. Keywords: Wild type control vs treated vs mutant Wild type untreated in triplicate is compared to wild type treated in triplicate along with three mutants in triplicate with and without treatment of indolicidin, totalling 30 samples

2008-04-06 | E-GEOD-8400 | biostudies-arrayexpress

The antimicrobial peptide-sensing system aps of Staphylococcus aureus

2008-04-07 | GSE8400 | GEO

MethylC-capture sequencing of control, osteoporotic, and Astragalus polysaccharides (APS)-treated osteoporotic SD rats

Project description:SD rats were intramuscular injected with dexamethasone to induce osteoporosis, and treated with APS. Then, colonic epithelia of control, osteoporotic and APS-treated osteoporotic rats were collected for MethylC-capture sequencing .

2023-08-03 | GSE155589 | GEO

Gene expression profiling in three inbred lines of maize affected by chilling treatment

Project description:We investigated chilling response of seedlings of three inbred maize lines: chilling tolerant S68911, chilling-sensitive S160 and moderate chilling-sensitive S50676. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (photoperiod 14/10h, temperature 24, light 250 umol quanta x m-2 x s-1), grown till the third-leaf stage and used in experiment. Chilling treatment started at the start of the dark period and lasted 38h (10h dark, 14h light,10h dark, 4h light). Growth conditions was as previously described but temperature was set to 14 (light/dark). At the same time control plants were grown as previously described. There were three biological replications of hybridization scheme.

2016-02-14 | E-MEXP-3508 | biostudies-arrayexpress

Microarray of blood samples of APS-1 patients and matched healthy controls

Project description:Autoimmune polyendocrine syndrome type I (APS-1) is a rare and devastating organ-specific autoimmune disease characterised by mutations in the Autoimmune Regulator (AIRE) gene. As AIRE is crucial for negative selection in the thymus, increased numbers of undesirable autoreactive T cells are released into the blood with the potential to cause tissue injury, including endocrine organ failure, chronic mucocutaneous candidiasis and hepatitis. B cells are also affected and produce high amounts of neutralising autoantibodies against both cytokines and organ-specific targets. The Aire-deficient mouse model has informed to some extent about immunological aspects of APS-1, but the rarity of APS-1 and inaccessibility of thymic tissue have severely limited immunological studies in patients. Sampling of APS-I patients and controls was performed in standardized manners in PAXgene blood RNA tubes (PreAnalytix, Qiagen, Hombrectikon, Switzerland) and stored at 80ºC until use. Purification of RNA was achieved by the PAXgene blood RNA kit following the instructions from the manufacturer. Samples were quality assessed by Agilent Bioanalyzer, using the Agilent 6000 Nano kit (Agilent, Santa Clara, CA, USA), providing RNA with RNA integrity numbers (RIN) above 6.0. The samples were randomly distributed into 4 batches for RNA extraction, each with 4 patients and 4 sex- and age matched controls and was extracted by the same person on the same day. Following the procedures from Illumina, RNA was subsequently transformed to cRNA, and these constructs were labeled, amplified and quality-checked again by the Agilent Bioanalyzer. The cRNAs were then hybridized to 4 Illumina HumanRef-8 BeadChip microarrays, followed by washing and scanning according to the protocol. Quality control of the arrays was done by BeadStudio.

2022-03-31 | E-MTAB-11630 | biostudies-arrayexpress

Autoimmune antigen and serum factor antigen reactivity in a cohort of patients with autoimmune polyendocrinopathy syndrome type 1(APS-1) and healthy controls.

Project description:The aim of the study was to test the hypothesis that APS-1 patient sera contains IgG reactivity to serum factor antigens concomitant with prototypical autoimmne antigens. We diluted patient sera 1:250 and incubated dilutions on a nitrocellulose-platform array printed with whole protein antigens. In this study, serum from 14 ndividuals (subsetted into APS-1 patient and healthy control categories) was profiled for IgG autoantibody reactivity to whole protein autoimmune and serum factor antigens. APS-1 patient sera was found using the significance analysis of microarrays (SAM) algorithm to be significantly more reactive with prototypical cytokine antigens previously identified as targets of autoantibodies.

2013-09-24 | E-GEOD-51101 | biostudies-arrayexpress

An analysis of the impact of infection by Buchnera aphidicola APS on gene expression of Drosophila S2 cells.

Project description:An analysis of the impact of infection by Buchnera aphidicola APS (isolated from Acyrthosiphon pisum strain LL01) on gene expression of S2 cells. All comparisons are made against a pool of RNA from S2 cells not exposed to B. aphidicola. B. aphidicola freshly isolated from the aphids, and data are collected at 1, 6 and 24 hours after exposure of S2 cells to the B. aphidicola preparation. Keywords: time course, Buchnera aphidicola APS, aphids, Drosophila melanogaster S2 cells

2008-12-15 | GSE11012 | GEO

Genetics of Antiphospholipid Antibody Syndrome (APS) - RTDC 5806

Project description:Genetics of Antiphospholipid Antibody Syndrome (APS) - RTDC 5806

| PRJNA497167 | ENA