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The use of Microarray Technology to screen for tumor related genes regulated in myeloid leukosis of chicken, during infection with avian leucosis virus subgroup J.

ABSTRACT: To survey avian leukosis virus subgroup J (ALV-J) integration in myeloid leukosis (ML) of chicken, we developed an ALV-J insertional identification platform based on hybrid-capture target enrichment and next-generation sequencing (NGS). In addition, we used gene expression profiling and bioinformatics to associate integration sites to transcriptional activity and to genetic features of the tumor cell genome. We selected six cases of ALV-J positive and diagnosed as ML for integration sites identify from commercial broiler breeder flocks in Guangdong Province of China between November 2011 and March 2012. All tumors were diagnosed on the basis of characteristic gross and microscopic lesions. Furthermore, PCR tests on the genomic DNA of tissues and virus isolation assay only showed ALV-J-specific positive results in previously study. We randomly chose 4 independent liver samples from the six cases for gene expression profile analysis. And 3 ALV-negative tissue samples from specific-pathogen-free (SPF) chickens at the same age were use as negative controls. Thus a total of 7 samples were hybridized, three representing control.

ORGANISM(S): Gallus gallus

SUBMITTER: yuhao li

PROVIDER: E-GEOD-48674 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The use of Microarray Technology to screen for tumor related genes regulated in myeloid leukosis of chicken, during infection with avian leucosis virus subgroup J.

Project description:To survey avian leukosis virus subgroup J (ALV-J) integration in myeloid leukosis (ML) of chicken, we developed an ALV-J insertional identification platform based on hybrid-capture target enrichment and next-generation sequencing (NGS). In addition, we used gene expression profiling and bioinformatics to associate integration sites to transcriptional activity and to genetic features of the tumor cell genome.

2013-07-11 | GSE48674 | GEO

Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chicken

Project description:Avian leukosis virus (ALV) causes substantial economic losses from mortality and decreased performance in poultry industry. To characterize the response to ALV challenge, we developed a novel methodology that combines four datasets: mRNA expression and their associated regulatory factors of miRNA and lncRNA, and ALV gene expression. Specific Pathogen-Free (SPF) layer chickens were assigned to the ALV-infected or control group. Spleen samples (n=6) were collected at 40 days post injection (dpi), and sequenced. Comparing the infected and non-infected groups, 864 genes, 7 miRNAs and 17 lncRNAs were differentially expressed.

2017-10-04 | E-MTAB-5135 | biostudies-arrayexpress

Distinctive microRNA profiles and target genes of aberrant microRNAs in leukemia chicken infected by subgroup J avian leukosis virus

Project description:Subgroup J avian leukemia is a type of oncology infectious disease caused by Subtype J of avian leukosis virus (ALV-J). It mainly encroaches on bone marrow cells, and metastasizes to liver, kidney, splenic ellipsoids and other organs, leading to myeloid leukosis (ML) and other malignancies, resulting in significant economic losses. microRNA play important roles in oncology infectious diseases. We used miRNA microarray analysis to detail the relationship of aberrant microRNAs and chicken ALV-J leukemia, and to try to find the potential diagnostic and therapeutic target for infections of subtype J of leukemia. ALV-J-infected and non-infected ten-week-old chicken liver tissues were sampled for the array assay. A1, A2, and A3 are the ALV-J infection group samples, and DA1, DA2, and DA3 are the control samples. 623 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different miRNA expressions were measured on the 7000HT Fast Real-Time PCR system.

2014-03-10 | E-GEOD-28434 | biostudies-arrayexpress

Distinctive microRNA profiles and target genes of aberrant microRNAs in leukemia chicken infected by subgroup J avian leukosis virus

2014-03-10 | GSE28434 | GEO

Genome-wide analyses of C. glutamicum SigH

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-24 | E-GEOD-52078 | biostudies-arrayexpress

WT vs gntR1 mutant gene expression profiles

Project description:The transcriptional regulator GntR1 downregulates the genes for gluconate catabolism and pentose phosphate pathway in Corynebacterium glutamicum. Gluconate lowers the DNA binding affinity of GntR1, which is probably the mechanism of gluconate-dependent induction of these genes. In addition, GntR1 positively regulates the ptsG, a gene encoding for a major glucose transporter, and the pck, a gene encoding phosphoenolpyruvate carboxykinase. Here, we searched for the new target of GntR1 at genome-wide scale by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis. This analysis identified 56 in vivo GntR1 binding sites, of which 7 sites were previously reported. The newly identified GntR1 sites include the upstream regions of carbon metabolism genes such as pyk, maeB, gapB, and icd. Binding of GntR1 to the promoter region of these genes was confirmed by electrophoretic mobility shift assay. The activity of the icd, gapB, and maeB promoters were reduced by the mutation at GntR1 binding site in contrast to the pyk promoter activity increased, indicating that GntR1 is a transcriptional activator of icd, gapB, and maeB and is a repressor of pyk. Thus, it is likely that GntR1 stimulates glucose uptake by inducing the phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) gene while repressing pyk to increase PEP availability in the absence of gluconate. Repression of zwf and gnd may reduce NADPH supply which may be compensated by the induction of maeB, and icd. Upregulation of icd, gapB, and maeB and downregulation of pyk by GntR1 probably supports gluconeogenesis. Gene expression profile of the wild type at the exponential phase was compared with that of the rshA deletion mutant. Three independent experiments were performed.

2014-07-15 | E-GEOD-58631 | biostudies-arrayexpress

ChIP-chip of Hmt1-9myc from S. cerevisiae

Project description:A comprehensive genome-wide binding profile for Hmt1 was obtained through the method of ChIP-chip using NimbleGen high-resolution tiling microarrays. Of the approximately 1000 Hmt1-binding sites found, the majority fall within or proximal to an ORF. However, Hmt1 occupancy is found at a number of other genomic features such as tRNA and snoRNA genes, thereby implicating a regulatory role in the biogenesis of these non-coding RNAs. RNA hybridization analysis shows that Hmt1 loss-of-function mutants display higher steady-state tRNA abundance relative to the wild-type. Co-immunoprecipitation studies show that Hmt1 interacts with the TFIIIB component Bdp1, suggesting a role for Hmt1 in modulating RNA pol III transcription to regulate tRNA production. ChIP-chip of Hmt1-9myc using Nimblegen high-resoluion tiling arrays

2012-12-25 | E-GEOD-40505 | biostudies-arrayexpress

Transcriptome analyses of the Corynebacterium glutamicum strains adapted to supraoptimal growth temperatures

Project description:C. glutamicum strains adapted to higher growth temperatures were obtained through an adaptive laboratory evolution experiment. To elucidate molecular basis for thermotolerance acquired by the evolved strains, we examined transcriptional responses of the evolved and parental strains to thermal stress using microarray technology. Each strain was grown at the optimal growth temperature (33 M-bM-^DM-^C). When OD610 reached around 7, the growth temperature increased to 41 M-bM-^DM-^C, and transcriptional changes of the evolved and parental strains were examined with microarray technology.

2015-01-06 | E-GEOD-64654 | biostudies-arrayexpress

Time-series of transcriptome analysis of Bacillus subtilis response to 25 mM potassium acetate and 0.85 M-BM-5M CCCP

Project description:The advent of M-bM-^@M-^XomicsM-bM-^@M-^Y techniques bear significant potential for the assessment of the microbiological stability of foods. This requires the integration of molecular data with their implication for cellular physiology. Here we performed a comparative physiological and transcriptional analysis of Bacillus subtilis stressed with three different weak organic acids: the commonly used food preservatives sorbic- and acetic- acid, plus the well-known uncoupler carbonyl cyanide-m-chlorophenyl hydrazone (CCCP). The concentration of each compound needed to cause a similar reduction of the growth rate negatively correlated with their membrane solubility, and positively with the concentration of undissociated acid. Intracellular acidification was demonstrated by expressing a pH-sensitive GFP derivative. The largest drop in intracellular pH was observed in CCCP-stressed cells and was accompanied by the transcriptional induction of the general stress response (GSR) and SigM regulon, responses known to be induced by acidification. The GSR was induced by acetate, but not by sorbate in mildly-stressed cells. Microarray analysis further revealed that all three acids activate transcriptional programs normally seen upon nutrient limitation and cause diverse responses indicative of an adaptation of the cell envelope. Based on the responses observed and the utilized pH measurements, the inhibitory effect of sorbic acid seems to be more focused on the cell membrane than that of acetic acid or CCCP. Time-series of B. subtilis response to 25 mM potassium acetate and 0.85 M-BM-5M CCCP during controlled growth in batch-fermentors in defined minimal medium (pH 6.4). Samples for microarrays were taken from both the treated and control cultures at 0, 10, 20, 30, 40, and 50 min after addition of acetate and CCCP. Two biologically independent experiments were performed.

2014-04-11 | E-GEOD-55051 | biostudies-arrayexpress

Identification of target genes of miR-193b

Project description:Searching of target genes of miR-193b by transcriptome assay using 44K Whole Human Genome Microarray system (Agilent Technologies, Palo Alto, CA) resulted in finding of several candidate genes. To search of targets genes of miR-193b, we performed transcriptome analysis to compare expression profiles between human pancreatic cancer cells, MIA PaCa-2, transfected with precursor of miR-193b and those transfected with a negative control precursor.

2012-03-14 | E-GEOD-25215 | biostudies-arrayexpress

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