Comparison of gene expression profiles in cultivated peanut (Arachis hypogaea L.) under strong artificial selection
Ontology highlight
ABSTRACT:
ORGANISM(S): Arachis hypogaea
SUBMITTER: Xiaoping Chen
PROVIDER: E-GEOD-30128 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The electroacupuncture-induced analgesic effect has been used widely to alleviate diverse pains. However, significant individual variations in analgesic effect of EA for both experiments and clinics were reported. According to the sensitivity of the analgesic response to EA stimulation, the subjects could be categorized into high responders (HR) and non responders (NR). However, the molecular mechanism of individual variability in the analgesic response to acupuncture stimulation is still uncertain. This study aims to investigate the potential gene expression in arcuate nucleus induced by 2Hz/100Hz electroacupuncture in HR and NR rats. Rats were given 2Hz or 100Hz electroacupuncture for 30 min and using cDNA microarrays to compare different gene expression in arcuate nucleus. Rats were exposed to different frequencies (2Hz or 100Hz) electroacupuncture stimulation for 30 min and nociceptive testing and returned to home cages for 1 hour before sacrificed. According to the sensitivity of the analgesic response to 2Hz or 100Hz EA stimulation, the rats divided into four groups: 2Hz-HR group, 2Hz-NR group, 100Hz-HR group and 100Hz-NR group. Subsequently analyzed their dorsal horn transcript profile using cDNA microarrays, the rats were without receiving electroacupuncture as control. The tissue of arcuate nucleus (Arc) of three rats was selected for transcript analysis in each group. The three control rats were mixed and labeled with cy5, each rat of experiment groups was labeled with cy3.
2011-07-07 | E-GEOD-30365 | biostudies-arrayexpress
Project description:Genetic variation amongst individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single-nucleotide changes. In this manuscript we explore variation on an intermediate scale-particularly insertions, deletions, and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number among individuals. Sequencing of a subset of structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence-map of human structural variation-an important standard for genotyping platforms and a prelude to future individual genome sequencing projects. Keywords: comparitive genomic hybridization, copy number variation, structural variation, fosmid end sequencing CGH analysis targeted against sites identified by fosmid end sequencing. 8 HapMap samples (sources of libraries ABC7-ABC14) are hybed against NA15510 (source of fosmid library G248).
2008-05-01 | E-GEOD-10037 | biostudies-arrayexpress
Project description:Transcriptional profiling of Schmidtea mediterranea planarians that have been amputated transversely and left to regenerate for different time points (UNIRR); the same experiment was performed on irradiated - neoblast depleted animals (IRR). The purpose of this experiment was to identify transcriptional changes that are induced within the first 12h following amputation. In order to distinguish between gene expression changes in the differentiated tissue and the neoblasts, a second set of time course data was created from irradiated animals Two-color experiment, 3 replicates per condition (including 10 animals/replica)
2012-04-29 | E-GEOD-36945 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE24575: Beta-arrestin-2 deficiency effect on intestinal tumorigenesis in Apc-mutated mice GSE24576: Gene expression analysis of tumors from ApcD14/+ mice Refer to individual Series
2012-01-20 | E-GEOD-24577 | 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:Bacteria can use host hormones as environment cue to modulate their pathogenic processes, which was discovered to play essential role in disease development. Actinobacillus pleuropneumoniae is one of the most important porcine respiratory pathogens causing great economic losses in the pig industry worldwide. Stress factors were found to contribute to the outcome of A. pleuropneumoniae infection. To test whether A. pleuropneumoniae could respond to host stress hormone catecholamines, the gene expression profiles after epinephrine (Epi) and norepinephrine (NE) treatment were compared with the untreated bacteria using microarray. Although the bacterial growth was not affected in the conditions tested, 157 and 104 genes associated with various function categories including many virulence factors were differentially expressed by Epi and NE treatment. 18 common genes were regulated by the two hormones, these genes included genes encoding virulence factors and potential responsors of Epi and NE. Further investigations on virulence traits demonstrated that cytotoxic activity was enhanced by Epi but repressed by NE in accordance with the regulations on apxIA. Biofilm formation was not affected by the two hormones despite that the biofilm formation gene pgaB was affected. Adhesion to host cells was induced by NE but not by Epi, possibly involving other putative adhesins affected by the hormones in addition to the autotransporter adhesin (APL_0443). Our study demonstrated that A. pleuropneumoniae could actively respond to catecholamines to control its virulence traits. The different regulated genes and effects caused by Epi and NE suggested A. pleuropneumoniae may have multiple responsive systems to sense different type of catecholamine hormones. Transcriptional profiles were analyzed using microarray to compared the epinephrine (Epi) or norepinephrine(NE) treated and untreated A. pleuropneumoniae. All samples were harvested from middle exponential phase (4 hours after sub-culture) at the OD600=1.435M-BM-10.065 for control, OD600=1.461M-BM-10.019 for Epi treated strain and OD600=1.545M-BM-10.115 for NE treated strain. Three biological replicates were conducted for each treatment. The total RNA were extracted and hybridized with the whole genome microarray of A. pleuropneumoniae. The signal intensities were normalized and transformed into log2 values. The genes with fold change M-bM-^IM-% 1.5 and P < 0.05 were selected as differentially expressed.
2012-03-19 | E-GEOD-25516 | biostudies-arrayexpress
Project description:StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase. The effect of stpA deletion on S. Typhimurium gene expression during growth in LB was analysed at 4 different time points (early-log, mid-log, late-log, and stationary phase) where the gene expression profile of the stpA-deletion strain was compared to that of the parental strain. Between two and three biological replicates were performed for each strain and time point. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.
2009-10-27 | E-GEOD-18424 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE18424: The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium GSE18428: StpA prevents RpoS-dependent transcription during mid-exponential growth in S. Typhimurium GSE18450: Identification of StpA-binding sites on the Salmonella genome Refer to individual Series
2010-06-21 | E-GEOD-18452 | biostudies-arrayexpress
Project description:Two prognostically significant subtypes of high-grade lung neuroendocrine tumors independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles. BACKGROUND: Classification of high-grade neuroendocrine tumors (HGNT) of the lung currently recognises large-cell neuroendocrine carcinoma (LCNEC) and small-cell lung carcinoma (SCLC) as distinct groups. However, a similarity in histology for these two carcinomas and uncertain clinical course have led to suggestions that a single HGNT classification would be more appropriate. Gene expression profiling, which can reproduce histopathological classification, and often defines new subclasses with prognostic significance, can be used to resolve HGNT classification. METHODS: We used cDNA microarrays with 40386 elements to analyze the gene expression profiles of 38 surgically resected samples of lung neuroendocrine tumors and 11 SCLC cell lines. Samples of large-cell carcinoma, adenocarcinoma, and normal lung were also included to give a total of 105 samples analyzed. The data were subjected to filtering to yield informative genes before unsupervised hierarchical clustering that identified relatedness of tumor samples. FINDINGS: Distinct groups for carcinoids, large-cell carcinoma, adenocarcinoma, and normal lung were readily identified. However, we were unable to distinguish LCNEC from SCLC by gene expression profiling. Three independent rounds of unsupervised hierarchical clustering consistently divided SCLC samples into two main groups with LCNEC samples largely integrated with these groups. Furthermore, patients in one of the groups identified by clustering had a significantly better clinical outcome than the other (83% vs 12% survived for 5 years; p=0.0094. None of the highly proliferative SCLC cell lines subsequently analyzed clustered with this good-prognosis group. INTERPRETATION: Our findings show that HGNT of the lung can be classified into two groups independent of SCLC and LCNEC. To this end, we have identified many genes, some of which encode well-characterized markers of cancer that distinguish the HGNT groups. These results have implications for the diagnosis, classification, and treatment of lung neuroendocrine tumors, and provide important insights into their underlying biology. Keywords: other
2004-02-10 | E-GEOD-1037 | biostudies-arrayexpress
Project description:We used aCGH data for detailed analysis of the natural killer gene complex (NKC) of multiple inbred strains, providing insight both into aCGH analysis of polymorphic gene clusters as well as structural information on the NKC itself. By unsupervised clustering analysis, the aCGH data can be precisely correlated with overall genome structural variation of the NKC as detected by RFLP variants in retrospective and prospective analyses. On a high resolution level, aCGH could be used to detect a small deletion within an NKC gene that is confined to only one mouse strain examined out of 22. The NKC region on mouse chromosome 6 is known to be an area with structural variation based on studies which reveal restriction fragment length polymorphic (RFLP) variants among inbred mouse strains. To verify predictive power of the unsupervised clustering algorithms, we prospectively collected aCGH data from two strains of mice (CBA/J, and NZW/LacJ) that were not among the original 20 strains (GEO accession # GSE10656) analyzed but represented strains whose Ly49 and Nkrp1 RFLP had been determined previously. We performed comparative genomic hybridization using a long-oligonucleotide array containing 2,149,887 probes evenly spaced across the reference genome with a median inter-probe spacing of 1,015 bases. Labeling, hybridization, washing, and array imaging were performed as previously described (PMID:18334530). To capture the variability along chromosome 6, the log2 signal ratios were organized into bins (a defined chromosome length in terms of bp). The entire chromosome was divided into consecutive bins, beginning with the position of the first probe. We used the variance of each bin to represent the variability along the chromosome. We performed two types of unsupervised clustering analysis of the log2 ratios of signal intensities of each probe (normalized). One is the non-hierarchical clustering using the partitioning among medoids (PAM) function as implemented in R's 'cluster' package. The other is the agglomerative hierarchical clustering based on the Euclidean distance. The average linkage method was used in clustering the strains as implemented in the hclust function in R's 'cluster' package.
2010-06-26 | E-GEOD-20090 | biostudies-arrayexpress