Gene expression profiling in Salmonella Typhimurium encountered with heterophils
Ontology highlight
ABSTRACT:
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium
SUBMITTER: Huaijun Zhou
PROVIDER: E-GEOD-16399 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To determine the host response to Salmonella Typhimurium (ST) in heterophils, a whole chicken genome array was used to analyze RNA isolated from heterophils stimulated in vitro with ST (30 min, 1 h, 2 h, and 3 h) or medium control (NS). Dual-color, direct comparisons were carried between ST-stimulated and non-stimulated controls (30 min vs. NS (30M/NS), 1 h vs. NS (1HR/NS), 2 h vs. NS (2HR/NS) and 3 h vs. NS (3HR/NS)). Each comparison includes four biological replicates. There were 2791, 3744, 12947 and 12482 genes differentially expressed in the comparisons of 30M/NS, 1HR/NS, 2HR/NS and 3HR/NS, respectively (P < 0.001) , while 50, 82, 153, and 146 genes were related to immune function, respectively. More than 80% of immune-related genes overlapped between the comparisons (30M/NS vs. 1HR/NS, 1HR/NS vs. 2HR/NS, and 2HR/NS vs. 3HR/NS). These candidate genes include cytokines (e.g. Interleukin (IL) 1β, -6, -10B and -12B), chemokines (e.g. IL-8, CCL4, K60 and K203) and cluster of differentiation (CD) markers (e.g. CD44, -47 and -83). A relatively large increase in the number of differentially expressed immune-related genes was observed between 1 h and 2 h post-stimulation. The results of continuous transcriptional change provide important information to elucidate both the cellular and molecular mechanisms of ST stimulation in chickens. Dual-color, common reference comparisons were carried between ST-stimulated (30M, 1HR, 2HR and 3HR) and non-stimulated controls (NS). Four biological replicates, with dye swap labeling, were included in the comparisons of each post-stimulation time point (30M/NS, 1HR/NS, 2HR/NS and 3HR/NS). Background subtracted signal intensity were collected from 16 arrays and normalized before data analysis.
2010-04-13 | E-GEOD-14684 | biostudies-arrayexpress
Project description:Chicken MarekM-bM-^@M-^Ys disease (MD) is a unique naturally occurring model for human herpesvirus-induced lymphomas that over-express the M-bM-^@M-^\HodgkinM-bM-^@M-^Ys disease antigenM-bM-^@M-^] (TNFRSF-8; CD30) on the lymphomaM-bM-^@M-^Ys neoplastically-transformed cells. We used transcriptomics, proteomics, computational systems biology and reductionist molecular biology to identify the differences between the CD30(hi) lymphoma cells and the non-transformed CD30(lo) MD lymphoma cells. We propose specific mechanisms of neoplastic transformation, genetic resistance to lymphomagenesis and impact of lymphoma microenvironment on CD30(hi) cell development. We demonstrate that: a) in situ, CD30(lo) cells are pre-neoplastic and we identify the proteome involved in transformation as well as potential mechanisms that may be controlled by MDV oncogene Meq; b) MD herpesvirus, (via its Meq oncogene) can drive a feed forward loop that induces CD30 transcription and overexpression, increased CD30 signaling, which then activates NFM-NM-:B and, in turn, increases Meq transcription; c) Meq transcriptional repression or activation from the CD30 promoter generally correlates with a polymorphism in the CD30 promoter between MD-resistant and -susceptible chicken genotypes and so a herpesvirus has evolved to utilize NFM-NM-:B as a direct transcriptional activator for its oncogene. A dual color, balanced design was carried on eight sorted lymphoma cells from white leghorn chickens infected with MDV GA/22 strain. Each of two sample types, CD30(hi) and CD30(lo) cells, includes four biological replicates for total RNA extraction and labeling. A Dye swap was used in four biological repeats of CD30(hi) to CD30(lo) cells comparison. Background subtracted signal intensities were collected from 4 arrays and normalized for data analysis.
2012-03-15 | E-GEOD-28034 | biostudies-arrayexpress
Project description:We conducted a genome-wide survey of genes in Ae. aegypti females that are transcriptionally responsive upon challenge with dengue virus (serotype-2). The array was designed with 60-mer oligos specific to 16,092 gene transcripts of gene build AaegL1.1 (www. vectorbase.org). The hybridizations were performed at NimbleGen. We provided total RNA purified from the infected and control samples to NimbleGen. To identify dengue-specific transcription response (DTR) genes of MS and MR females upon infection with DENV2-JAM1409, a total of 15 independent samples (12 test samples and 3 control samples) were used for array hybridizations. These consisted of four DENV2 infected samples (MS-3hr, MR-3hr, MS-18hr and MR-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Three independent biological replicates were prepared for each of the above five samples were used for hybridizations. The Ae. aegypti genes responsive to dengue infection were identified in MOYO-S (MS) and MOYO-R (MR) females, upon challenging them with DENV serotype-2, by a genome-wide transcriptome analysis carried out using the NimbleGen oligonucleotide microarray format. We profiled gene expressions of Aedes aegypti mosquitoes, strain MOYO-S (MS, susceptible to dengue virus) and MOYO-R (MR, refractory to dengue virus) at 3 hr and 18 hr after infection with dengue virus (seroptype-2). The test samples were prepared in parallel to the control samples. The control samples were derived from females fed with normal blood that was not mixed with dengue (mock infection). The test samples were prepared from females that were fed with blood mixed with dengue virus (infectious meal). A total of 12 test samples were prepared that represented three biological replicates of dengue infected MS females at 3hr and 18 post-infection times; and MR females at 3hr and 18hr post-infection times. The test samples were compared to a common uninfected control that was prepared by pooling equal amount RNA of the individual control of both strains and both post-infection time points (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr). The control-pool strategy ensured us to identify genes that were responsive in response to dengue infection but not due to genetic differences between the two strains or developmental changes between the two post-infection time points. A total of 3 control pools were used in our array expression studies. Control-1 was prepared from RNA isolated from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the first biological replication. Similarly, control-2 was prepared from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the second biological replication. And control-3 was prepared from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the third biological replication. Thus, the three control pools represented three biological replicates corresponding to the three biological replicates of the test samples.
2011-09-29 | E-GEOD-16563 | biostudies-arrayexpress
Project description:Environmental reproductive health focuses on the effect of exposure to contaminants considered as endocrine disruptors. Developmental testis is considered as target of these compounds affecting testicular functions in adults and suspected implications in tumor etiology. Comparative analysis of gene expression in mouse testis exposed to five disruptors, three different dosages and three accumulative developmental stages shown defined signature profiles of gene deregulation for MEHP (monoethyl phthalate) and zearalenone (a phytoestrogen) and different to 17β-estradiol exposure. The effects are even detected in postpuberal male offspring from premating exposed mothers. Oxidative stress response, protein ubiquitination and oxidative phosphorylation are the most representative pathways affected. Animal Exposure CD-1 mice were in vivo exposed to several doses of EDs following a defined protocol: mothers were exposed two weeks before mating (exposure A); the same exposure and dose were maintained during pregnancy (exposure B) and four weeks after birth (exposure C). In all exposures, male offspring were sacrificed to obtain the testes. The compounds were administrated in drinking water to a final concentration of: E2(mg/l) BPA(mg/l) Zea(mg/l) MEHP(mg/l) Lindane(mg/l) Dose (1) 0.02 0.5 4 27.85 50 Dose (2) 0.04 50 12 139.17 100 Dose (3) 0.16 200 20 278.34 200 Ethanol was used as vehicle for E2, BPA and Zea and DMSO was for MEHP and Lindane. Control testes were obtained from animals exposed to solvents of EDs: Ethanol and DMSO. Animal care and sacrifice were made following regulations from the CSIC Bioethics Committee. RNA preparation Total RNA from testes of exposed animals and controls was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s standard protocol. RNA samples were spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). To minimize the effect of inter-individual expression variability we made pools of RNA from at least 3 individual RNA samples from each experimental condition (same quantity of total RNA per sample). Pools of RNA were checked for quality performing Experion analysis (Bio-Rad Laboratories). Total RNA from testes of unexposed four weeks old animals was also extracted with the purpose of making pools to assess the variability at the expression level of the mouse strain used (Ctr). Microarray Processing Starting with total RNA from pools described above, full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). The same dye signal quantities of labeled experimental and control aRNAs were mixed and hybridized to Mouse Oligoset v3 (OPERON) arrays from Genomics facility-University of Cincinnati (USA). The slides contained 31,769 spotted probes (70 mer oligonucleotides) corresponding to 24,878 expressed or predicted mouse genes. Hybridization and washes of microarrays were performed according to Genomics facility-University of Cincinnati instructions. Dye-Swap replicates were performed: one slide hybridized with experimental and control targets labeled with Cy3 and Cy5, respectively; and the second slide with the same type of targets but inversely labeled. Target refers to labeled aRNA while probe refers to the oligonucleotides spotted on the microarray platform. Imaging and data generation were carried out using a GenePix 4000B (Axon Instruments) and associated software from Axon Instruments, Inc. The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5. Images were captured in TIFF files. Information extraction for a given spot was based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots. The Cy3 and Cy5 fluorescence signal intensities were normalized.
2010-06-01 | E-GEOD-14774 | biostudies-arrayexpress
Project description:Gene expression profiling of clostridium perfringens infection in broilers on medicated and non-medicated diets using chicken 44k agilent microarray. To elucidate molecular and ceelular mechanisms of bacitracin effect on CP infection in chickens by microarray technology. A total number of 600 Ross broilers were reared in 12 pens with each hosting 50 birds. Each 6 pens of birds were fed bacitracin-medicated (55 ppm) or non-medicated starter diets immediately after the chicks were placed. At day 18, birds were challenged with CP. Spleens were collected from 12 birds of each group at day 18 (before infection), 19, 20, and 22. Total RNA was labeled by Cy3 or Cy5 with dye swap. Gene signal intensity was globally normalized by LOWESS and expressed on natural log scale. A mixed model including treatment, time, array (random effect), dye, and all interactions among treatment, time was used to identify differentially expressed genes between treatments, at the 1% significance level.
2009-09-01 | E-GEOD-14759 | biostudies-arrayexpress
Project description:Mice were intranasally instilled at 6 weeks of age with silica, titanium dioxide, or saline control and macrophages were harvested by broncho-alveolar lavage at 14 weeks of age. RNA was isolated using RNeasy Mini kits (Qiagen). Due to low yield of RNA, mRNA was amplifed by RiboAmp kits (Arcturus) and resulting aRNA was indirectly labeled with Alexa-Fluor 647 dye (Molecular Probes). This was hybridized against Universal Mouse Reference RNA (Stratagene) which was indirectly labeled with Alexa-Fluor 555 dye (Molecular Probes). Slides were printed in house using PCR product cDNA targets on GAPS slides (Corning). Slides were scanned with an Axon GenePix 4000B scanner and data was analyzed using GenePix Pro 4.0 software and Iobion GeneTraffic Duo software. Data was normalized to a total 1:1 ratio of read to green dye.
2010-06-10 | E-GEOD-2279 | biostudies-arrayexpress
Project description:Homemade weekend free media are a promising way for the labs to reduce the manpower and high costs associated with the culture of human induced pluripotent stem cells (hiPSCs) in feeder-free conditions. However, as these media would have a different concentration of various growth factors, cells may perceive a change in the signalling environments and change their transcription profile. To investigate the extent of this change, we decided to perform RNA sequencing and study the change of gene expression as compared to cells grown in commercial, daily changed E8.
2024-07-11 | E-MTAB-14237 | biostudies-arrayexpress
Project description:To explore the effects on the NF-kB transcriptome after knockdown of RPS3 in stimulated T cells, we performed microarray assays comparing RPS3-silenced versus NS-treated samples on the same chip. p65-silenced versus NS-treated samples were used as a control. Keywords: time series design Jurkat cells transfected with control siRNA versus RPS3 or p65-siRNA were stimuated with TCR for 1, 3, or 6 hours for a total of 6 arrays.
2010-05-26 | E-GEOD-7231 | biostudies-arrayexpress
Project description:Chicken 60-mer oligonucleotide microarray, including 39854 cDNA and ESTs, entire Marek’s disease virus and avian influenza virus genomes, and 150 chicken microRNAs, was developed. Cecal tonsil, ileum, liver and spleen from 6 chickens were selected for hybridization to validate the microarray performance. There are 2886, 2886, 2660, 358, 3208 3355, and 3710 genes significantly expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum at the P<10-7. Number of tissue specific genes for cecal tonsil, ileum, liver and spleen was 95, 71, 535, and 108, respectively with p < 10-7. More than 95% of spots had high SNR (>10). Keywords: characteristics of newly developed microarray using different normal tissue Loop design was carried on for all of tissue samples from the six chickens. Samples of four tissues from a chicken were used in each loop. The order of the tissues in each loop was changed so that all pairs of tissues were combined on an array with an equal number of times. Dye swap was used so that each tissue was measured an equal number of times with each dye. Data from 12 measurements for each tissue were collected, in total, 48 measurements from 24 arrays.
2008-02-28 | E-GEOD-7452 | biostudies-arrayexpress
Project description:This experiment utilized rat fibroblasts that are wild-type for c-Myc (TGR-1 cells) and null for c-Myc (HO15.19 cells). Both were treated treated with rapamycin for 24 hr (comparison group, vehicle control). Cells were studied under conditions that supported proliferation. Rapamycin (50nM or DMSO vehicle control) was added for 24 hr after which RNA was prepared and analyzed.
2010-10-25 | E-GEOD-18845 | biostudies-arrayexpress